Human

mass

balance

study

of

the

novel

anticancer

agent

ixabepilone

using

accelerator

mass

spectrometry

Summary

Introduction

The

taxanes

paclitaxel

and

docetaxel

are

important

anti-cancer

drugs

-LSB-

-RSB-

However

their

use

is

complicated

by

low

oral

bioavailability

and

the

development

of

resistance

due

to

over-expression

or

β-tubulin

mutation

-LSB-

-RSB-

A

search

for

microtubule

stabilizing

agents

with

improved

characteristics

compared

to

taxanes

led

to

the

discovery

of

epothilone

A

and

B

in

extracts

of

the

myxobacterium

Sorangium

cellulosum

-LSB-

-RSB-

which

were

subsequently

shown

to

bind

to

tubulin

at

the

same

binding

site

as

paclitaxel

-LSB-

-RSB-

In

vitro

epothilone

B

was

more

active

than

in

vivo

-LRB-

mouse

models

-RRB-

-LSB-

-RSB-

and

in

vivo

hydrolysis

of

the

lactone

ring

was

suspected

of

producing

inactive

metabolites

To

improve

the

metabolic

stability

of

the

naturally

occurring

epothilones

these

were

modified

by

replacing

the

ester

bond

with

an

amide

bond

-LSB-

-RSB-

In

general

lactam

analogues

displayed

tubulin-polymerizing

and

cytotoxic

potencies

inferior

to

their

naturally

occurring

counterparts

The

exception

to

this

rule

was

the

lactam

analogue

of

epothilone

B

ixabepilone

-LRB-

NSC

EpoB-lactam

aza-EpoB

B

-RRB-

see

Fig.

for

structure

-LSB-

-RSB-

Ixabepilone

has

undergone

a

number

of

phase

II

clinical

trials

with

varying

schedules

at

doses

from

to

administered

as

an

intravenous

infusion

over

to

h

-LSB-

-RSB-

Response

rates

in

metastatic

breast

-LRB-

-RRB-

non-small

cell

lung

-LRB-

-RRB-

hormone-refractory

metastatic

prostate

cancer

-LRB-

-RRB-

and

metastatic

renal

cell

carcinoma

-LRB-

-RRB-

were

modest

to

promising

and

warrant

further

investigation

-LSB-

-RSB-

The

pharmacokinetics

of

ixabepilone

have

been

described

-LSB-

-RSB-

and

the

contribution

of

two

known

chemical

degradation

products

was

shown

to

be

negligible

-LSB-

-RSB-

however

other

than

that

it

is

a

substrate

-LSB-

-RSB-

little

is

known

about

the

excretion

and

metabolic

fate

of

ixabepilone

Fig.

structures

of

epothilone

B

and

its

lactam

analogue

ixabepilone

The

present

investigation

was

aimed

at

determining

the

pharmacokinetics

and

excretory

pathways

of

-LSB-

-RSB-

ixabepilone

To

this

end

we

initiated

a

mass

balance

study

of

ixabepilone

in

humans

A

mass

balance

is

an

elaborate

pharmacokinetic

investigation

employing

a

radioactive

tracer

It

investigates

the

plasma

pharmacokinetics

and

excretion

of

both

the

unchanged

drug

and

the

total

radioactivity

-LRB-

drug

and

metabolites

-RRB-

and

allows

elucidation

of

the

metabolic

fate

of

a

drug

The

main

objective

is

the

maximum

recovery

of

the

radioactive

dose

in

urine

and

faeces

-LSB-

-RSB-

Due

to

autoradiolysis

-LSB-

-RSB-

ixabepilone

at

a

typical

specific

activity

of

μCi/mg

was

unstable

However

-LSB-

-RSB-

ixabepilone

at

a

specific

activity

of

less

than

nCi/mg

was

found

to

be

stable

Therefore

a

study

was

conducted

with

a

low

radioactive

dose

of

nCi

of

as

opposed

to

a

more

typical

human

radio-tracer

dose

of

circa

μCi

dosed

in

study

For

detection

of

these

very

low

levels

of

radioactivity

we

used

an

ultra-sensitive

detection

method

Accelerator

Mass

Spectrometry

-LRB-

AMS

-RRB-

-LSB-

-RSB-

which

measures

the

amount

of

as

if

it

were

a

stable

isotope

label

instead

of

measuring

its

decay

AMS

separates

elemental

isotopes

through

differences

in

mass

charge

and

energy

resulting

in

a

-LSB-

-RSB-

-LSB-

-RSB-

isotope

ratio

Subtracting

the

natural

-LSB-

-RSB-

background

level

and

taking

into

account

the

total

carbon

content

of

the

sample

results

in

a

total

-LSB-

-RSB-

amount

that

is

converted

to

a

conventional

unit

for

radioactivity

-LRB-

DPM

Bq

or

Ci

-RRB-

Given

the

very

low

dose

of

radioactivity

administered

-LRB-

nCi

compared

to

μCi

in

a

typical

radio-tracer

study

-RRB-

administration

would

result

in

negligible

radiation

exposure

Materials

and

methods

Study

design

This

was

an

open-label

single-dose

study

in

which

eight

patients

with

histologically

confirmed

solid

tumours

received

an

intravenous

fixed

dose

of

mg

nCi

-LSB-

-RSB-

ixabepilone

over

h

The

protocol

and

informed

consent

form

were

reviewed

and

approved

by

the

Institutional

Review

Board

of

the

Antoni

van

Leeuwenhoek

Hospital/The

Netherlands

Cancer

Institute

and

each

patient

gave

written

informed

consent

before

receiving

the

study

medication

Eligibility

criteria

most

relevant

to

the

mass

balance

study

were

availability

for

in-house

admittance

during

the

first

days

adequate

hepatic

and

renal

function

a

performance

status

-LRB-

PS

-RRB-

of

and

a

life

expectancy

of

at

least

weeks

Patients

Eight

patients

-LRB-

three

male

and

five

female

-RRB-

with

a

median

age

of

years

and

a

WHO

performance

status

of

were

enrolled

in

the

study

All

patients

had

advanced

cancer

for

which

no

standard

anti-cancer

therapy

was

available

The

primary

tumours

were

squamous

cell

carcinoma

colon

cancer

-LRB-

n

-RRB-

gastric

carcinoma

ovarian

cancer

non-small

cell

lung

cancer

sigmoid

adenocarcinoma

and

pancreas

carcinoma

Study

medication

Individual

vials

of

radiolabeled

ixabepilone

contained

mg

nCi

-LSB-

-RSB-

ixabepilone

-LRB-

specific

activity

nCi/mg

-RRB-

The

-LSB-

-RSB-

ixabepilone

was

synthesized

by

Bristol-Myers

Squibb

by

growing

the

myxobacterium

Sorangium

cellulosum

in

containing

medium

This

resulted

in

labeling

throughout

the

ixabepilone

molecule

Radiochemical

and

chemical

purity

was

confirmed

at

Vials

were

reconstituted

using

ml

Cremophor

EL

ethanol

-LRB-

v/v

-RRB-

each

A

ml

volume

of

the

reconstituted

-LSB-

-RSB-

ixabepilone

was

added

to

ml

Lactated

Ringer

's

Infusion

-LRB-

LRI

-RRB-

After

mixing

a

ml

sample

was

taken

for

quantitation

of

radioactivity

by

liquid

scintillation

counting

-LRB-

LSC

-RRB-

LSC

radioactivity

values

were

recalculated

to

amounts

of

-LSB-

-RSB-

ixabepilone

for

use

in

calculating

recovery

from

feces

and

urine

After

the

intravenous

administration

infusion

lines

were

flushed

with

ml

LRI

Gravimetric

measurements

of

the

infusion

flask

prior

to

and

after

administration

enabled

calculation

of

the

amount

of

radioactivity

actually

administered

To

prevent

Cremophor

EL-related

hypersensitivity

reactions

patients

were

pre-medicated

with

oral

and

blockers

Sample

collection

Blood

was

collected

at

-LRB-

pre-dose

-RRB-

-LRB-

prior

to

end

of

infusion

-RRB-

and

h

after

start

of

infusion

An

indwelling

catheter

contra-lateral

to

the

administration

site

was

used

for

serial

blood

sampling

Separate

but

simultaneous

blood

samples

were

taken

for

the

quantitation

of

total

radioactivity

and

unchanged

ixabepilone

respectively

Plasma

was

obtained

by

immediate

centrifugation

of

the

blood

-LRB-

min

g

°C

-RRB-

The

plasma

layer

was

aspirated

and

stored

below

°C

until

analysis

We

collected

complete

urinary

and

faecal

output

up

to

days

after

administration

Urine

was

collected

over

intervals

in

refrigerated

collection

jugs

At

the

end

of

each

collection

interval

the

respective

urine

samples

were

mixed

and

total

volume

was

recorded

Aliquots

were

stored

below

°C

until

analysis

Faecal

samples

were

collected

and

stored

at

°C

per

portion

and

combined

per

interval

Faeces

were

homogenized

after

addition

of

water

-LRB-

w/w

-RRB-

Aliquots

were

stored

below

°C

until

analysis

AMS

analysis

of

total

radioactivity

-LRB-

TRA

-RRB-

in

plasma

urine

and

faeces

TRA

in

plasma

urine

and

faeces

was

determined

using

AMS

-LRB-

Exceleron

York

UK

-RRB-

-LSB-

-RSB-

Briefly

sample

pre-treatment

consisted

of

the

conversion

of

the

carbon

within

the

samples

to

graphite

via

a

two-step

process

of

oxidation

and

reduction

-LSB-

-RSB-

Oxidation

-LRB-

combustion

-RRB-

was

performed

by

heating

the

dried

sample

with

copper

oxide

under

vacuum

at

°C

for

h

in

a

heat-sealed

tube

Reduction

-LRB-

graphitisation

-RRB-

was

performed

by

heating

the

carbon

dioxide

formed

from

the

oxidised

sample

with

zinc

titanium

hydride

and

cobalt

at

°C

for

h

followed

by

a

further

h

at

°C

After

the

graphitisation

process

the

graphite

was

pressed

into

a

cathode

In

the

AMS-procedure

this

cathode

was

bombarded

with

high-energy

caesium

-LRB-

Cs

-RRB-

ions

The

resulting

negative

carbon

ion

beam

was

introduced

into

the

AMS

instrument

accelerated

by

an

electric

field

of

MV

and

the

carbon

atoms

were

stripped

of

their

valency

electrons

This

resulted

in

separation

of

the

carbon

isotopical

elements

as

ions

The

carbon

isotopes

and

were

quantitated

using

Faraday

cups

while

was

quantitated

by

a

gas

ionization

detector

Because

AMS

provides

an

isotope

ratio

that

is

-LSB-

-RSB-

-LSB-

-RSB-

and

not

an

absolute

value

it

is

necessary

to

know

the

carbon

content

of

the

sample

plus

any

added

carrier

This

was

determined

using

a

carbon

hydrogen

nitrogen

analyser

-LRB-

Elemental

Microanalysis

Ltd.

Okehampton

UK

-RRB-

The

natural

background

-LSB-

-RSB-

-LSB-

-RSB-

level

per

matrix

was

subtracted

to

obtain

the

amount

of

ixabepilone-related

The

total

carbon

content

and

the

specific

activity

of

-LSB-

-RSB-

ixabepilone

was

used

to

convert

the

-LSB-

-RSB-

-LSB-

-RSB-

ratio

to

ixabepilone

equivalents

-LRB-

ng/ml

sample

or

of

dose

-RRB-

Using

this

sophisticated

technique

it

was

possible

to

quantitate

DPM/ml

plasma

DPM/ml

urine

and

DPM/g

faeces

-LRB-

DPM

corresponds

to

ng

-LSB-

-RSB-

ixabepilone

-RRB-

Analysis

of

ixabepilone

in

plasma

and

urine

Concentrations

of

ixabepilone

parent

drug

in

plasma

and

urine

were

determined

with

a

validated

liquid

chromatography

assay

equipped

with

tandem

mass

spectrometric

detection

-LRB-

Bristol-Myers

Squibb

Princeton

NJ

-RRB-

Briefly

after

addition

of

internal

standard

-LRB-

-RRB-

to

ml

of

each

sample

calibration

standard

and

quality

control

sample

the

samples

were

precipitated

with

acetone

The

supernatant

was

further

extracted

with

The

organic

layer

was

removed

and

evaporated

to

dryness

The

residue

was

reconstituted

and

injected

into

the

LC-MS/MS

system

Chromatographic

separation

was

achieved

isocratically

on

a

YMC

ODS-AQ

column

-LRB-

mm

internal

diameter

-RRB-

at

a

flow

rate

of

ml/min

with

detection

by

electrospray

tandem

mass

spectrometry

The

mobile

phase

contained

acetonitrile

M

ammonium

acetate

-LRB-

pH

-RRB-

-LRB-

v/v

-RRB-

The

standard

curve

which

ranged

from

to

ng/ml

was

constructed

with

a

weighted

quadratic

regression

model

The

within-run

precision

for

ixabepilone

in

plasma

and

urine

was

within

and

respectively

The

between-run

precision

for

ixabepilone

in

plasma

and

urine

was

within

and

respectively

The

accuracy

was

within

and

of

the

nominal

values

in

plasma

and

urine

respectively

Pharmacokinetic

analyses

The

pharmacokinetic

analyses

of

the

ixabepilone

plasma

concentration

versus

time

data

were

performed

by

non-compartmental

methods

using

Kinetica

Version

-LRB-

InnaPhase

Corporation

Philadelphia

PA

-RRB-

The

peak

plasma

concentration

-LRB-

Cmax

-RRB-

and

the

time

to

reach

maximal

concentration

-LRB-

Tmax

-RRB-

represent

observed

values

The

area

under

the

plasma

concentration

versus

time

curve

-LRB-

AUC

-RRB-

was

calculated

using

a

combination

of

linear

and

log

trapezoidal

summations

The

AUC

was

extrapolated

to

infinity

-LRB-

AUCinf

-RRB-

by

dividing

the

last

measurable

concentration

by

the

terminal

rate

constant

k

The

absolute

value

of

k

was

used

to

estimate

the

apparent

terminal

half-life

ln

k

The

total

body

clearance

-LRB-

Cl

-RRB-

was

determined

by

dividing

dose

by

AUCinf

and

the

volume

of

distribution

at

steady-state

-LRB-

Vss

-RRB-

was

calculated

as

dose

area

under

the

moment

curve

-LRB-

AUMCinf

-RRB-

-LRB-

AUCinf

-RRB-

with

appropriate

corrections

for

infusion

duration

Renal

clearance

was

calculated

by

dividing

amount

excreted

by

the

AUC

Similarly

pseudopharmacokinetic

parameters

were

calculated

for

TRA

Outliers

were

statistically

assessed

using

Dixon

's

Q

test

Results

To

evaluate

the

pharmacokinetics

and

excretory

pathways

of

-LSB-

-RSB-

ixabepilone

we

performed

a

mass

balance

study

in

eight

patients

Figure

shows

the

mean

plasma

concentrations

over

time

of

both

TRA

and

ixabepilone

as

determined

by

AMS

and

LC-MS/MS

respectively

Fig.

-LRB-

SD

-RRB-

plasma

concentration-time

curves

of

-LSB-

-RSB-

ixabepilone

derived

radioactivity

-LRB-

filled

square

-RRB-

and

unchanged

-LSB-

-RSB-

ixabepilone

-LRB-

open

square

-RRB-

for

eight

patients

Both

TRA

and

ixabepilone

in

plasma

exhibited

an

initial

distribution

phase

of

approximately

h

followed

by

a

much

slower

terminal

elimination

phase

with

half-lives

of

and

h

respectively

The

time

to

maximum

plasma

concentration

was

typically

around

the

end

of

infusion

Plasma

ixabepilone

concentrations

were

quantifiable

through

h

in

all

patients

and

plasma

TRA

concentrations

were

quantifiable

through

h

in

all

patients

except

in

patient

in

whom

plasma

TRA

concentrations

were

only

quantifiable

for

h.

Pharmacokinetic

parameters

are

summarized

in

Table

The

ratio

of

the

ixabepilone

AUC

to

the

total

radioactivity

AUC

or

AUC-ratio

is

a

measure

of

exposure

to

-LSB-

-RSB-

ixabepilone

relative

to

total

-LSB-

-RSB-

ixabepilone

related

compounds

The

AUC

ratio

of

patient

was

larger

than

unity

This

was

caused

by

the

underestimated

TRA

AUC

which

was

based

on

measurements

until

only

h

after

which

plasma

concentrations

fell

below

the

lower

limit

of

quantitation

Besides

the

TRA

AUC

the

of

patient

was

also

inaccurately

estimated

at

h.

Therefore

patient

was

omitted

from

calculation

of

mean

plasma

TRA

parameters

Figure

shows

the

plasma

concentrations

of

ixabepilone

relative

to

TRA

for

patients

and

patient

Patient

experienced

a

blocked

bile

duct

-LRB-

reflected

by

a

maximum

plasma

bilirubin

concentration

of

μmol/l

-LRB-

upper

limit

of

normal

-RRB-

and

alkaline

phosphatase

of

U/l

-LRB-

upper

limit

of

normal

-RRB-

at

day

-RRB-

resulting

in

a

higher

plasma

TRA

Cmax

and

AUC

The

higher

TRA

plasma

concentrations

in

patient

resulted

in

an

AUC

ratio

of

plasma

ixabepilone

to

TRA

that

was

lower

than

that

of

the

other

patients

In

contrast

unchanged

ixabepilone

plasma

pharmacokinetics

were

not

affected

in

this

patient

Table

pharmacokinetic

parameters

of

ixabepilone

and

total

radioactivity

in

cancer

patients

after

a

h

intravenous

infusion

of

mg

nCi

-LSB-

-RSB-

ixabepiloneNrIxabepiloneRadioactivity

-LRB-

ixabepilone

equiv

-RRB-

AUClast

ratioaCmax

-LRB-

ng/ml

-RRB-

AUClast

-LRB-

μg

h/ml

-RRB-

AUCinf

-LRB-

μg

h/ml

-RRB-

-LRB-

h

-RRB-

Cl

-LRB-

l/h

-RRB-

Vss

-LRB-

l

-RRB-

Cmax

-LRB-

ng/ml

-RRB-

AUClast

-LRB-

μg

h/ml

-RRB-

AUCinf

-LRB-

μg

h/ml

-RRB-

-LRB-

h

-RRB-

12773.063.3551.720.912753221.891.968.31.62

baAUClast

ratio

is

calculated

by

dividing

AUClast

ixabepilone

by

AUClast

TRA

and

expresses

the

relative

contribution

of

ixabepilone

to

TRA

exposure

in

plasma.bPatient

was

not

included

in

the

calculation

because

the

radioactivity

AUC

and

could

not

be

determined

accurately

-LRB-

see

text

-RRB-

This

also

resulted

in

the

deviating

AUClast

ratio

-LRB-

outlier

-RRB-

Fig.

-LRB-

SD

-RRB-

-LSB-

-RSB-

ixabepilone

to

total

radioactivity

ratio

in

plasma

over

time

for

patients

-LRB-

filled

square

-RRB-

and

patient

-LRB-

open

square

-RRB-

Figure

displays

the

mean

excretion

of

TRA

in

urine

and

faeces

and

the

total

in

time

and

Fig.

displays

the

mean

cumulative

urinary

excretion

of

-LSB-

-RSB-

ixabepilone

derived

radioactivity

and

unchanged

-LSB-

-RSB-

ixabepilone

Table

shows

individual

h

excretions

of

-LSB-

-RSB-

ixabepilone

and

TRA

in

urine

and

faeces

The

U/F

ratio

is

the

ratio

of

urinary

recovery

relative

to

faecal

recovery

Patient

displayed

a

rather

low

recovery

of

radioactivity

from

both

urine

-LRB-

-RRB-

and

faeces

-LRB-

-RRB-

Plasma

pharmacokinetics

were

not

different

compared

to

the

other

patients

A

low

total

recovery

of

was

also

obtained

for

patient

attributable

to

a

very

low

faecal

recovery

-LRB-

-RRB-

while

urinary

recovery

was

normal

-LRB-

-RRB-

This

patient

only

defecated

at

h

and

at

h

-LRB-

a

few

grams

-RRB-

which

almost

certainly

explains

the

observed

low

recovery

Although

the

plasma

pharmacokinetics

and

urinary

excretion

did

not

deviate

extremely

from

the

other

patients

patient

displayed

a

somewhat

elevated

plasma

exposure

to

both

radioactivity

and

ixabepilone

and

the

lowest

clearance

for

unchanged

ixabepilone

If

we

now

look

at

the

U/F

ratios

-LRB-

a

measure

of

urinary

versus

faecal

elimination

-RRB-

patient

who

had

the

low

fecal

output

is

an

outlier

-LRB-

Q

critical

value

p

-RRB-

compared

to

patients

and

Patient

who

experienced

the

blocked

bile

duct

stent

is

also

an

outlier

-LRB-

Q

critical

value

p

-RRB-

compared

to

the

same

patients

The

urinary

recovery

of

patient

was

highest

at

causing

the

large

standard

deviation

of

urinary

recovery

However

the

urinary

recovery

of

unchanged

ixabepilone

of

was

within

the

normal

range

The

faecal

recovery

of

this

patient

was

the

lowest

-LRB-

excluding

patient

-RRB-

at

Apparently

there

was

no

accumulation

of

the

active

drug

despite

a

decreased

biliary

excretion

Fig.

urinary

-LRB-

open

square

SD

-RRB-

faecal

-LRB-

open

circle

SD

-RRB-

and

total

-LRB-

filled

square

SD

-RRB-

cumulative

excretion

-LRB-

h

-RRB-

of

-LSB-

-RSB-

ixabepilone

derived

radioactivity

for

eight

patientsFig

-LRB-

SD

-RRB-

cumulative

urinary

excretion

of

-LSB-

-RSB-

ixabepilone

derived

radioactivity

-LRB-

filled

square

-RRB-

and

unchanged

-LSB-

-RSB-

ixabepilone

-LRB-

open

square

-RRB-

for

eight

patientsTable

and

faecal

recovery

-LRB-

h

-RRB-

of

ixabepilone

and

total

radioactivity

in

cancer

patients

after

a

h

intravenous

infusion

of

mg

nCi

-LSB-

-RSB-

ixabepiloneNraRecovery

-LRB-

of

dose

-RRB-

Radioactivity

-LRB-

U/F

ratioc

-RRB-

Ixabepilone

-LRB-

Clrenal

-LRB-

l/h

-RRB-

-RRB-

IxabepiloneTotal

aPatients

and

were

male.bPatient

was

not

included

because

of

the

extremely

low

production

of

faeces

and

patient

was

not

included

in

the

calculation

because

his

bile

duct

obstruction

-LRB-

relevance

illustrated

by

increasing

plasma

bilirubin

concentrations

-RRB-

may

have

reduced

faecal

excretion.cThe

U/F

ratio

is

the

ratio

of

urinary

recovery

relative

to

faecal

recovery

On

average

more

than

of

the

drug

was

excreted

over

the

period

with

the

majority

of

being

excreted

in

faeces

and

in

urine

Excretion

in

faeces

occurred

at

a

relatively

constant

rate

over

the

entire

collection

period

with

only

and

of

dose

recovered

in

the

and

h

collection

intervals

respectively

In

contrast

urinary

excretion

displayed

two

distinct

phases

with

of

total

urinary

radioactivity

-LRB-

corresponding

to

of

dose

-RRB-

and

of

total

urinary

ixabepilone

being

excreted

in

the

first

h.

From

to

h

urinary

excretion

occurred

at

a

relatively

slow

constant

rate

This

may

reflect

the

biphasic

plasma

curve

with

high

concentrations

in

the

distribution

phase

and

lower

concentrations

in

the

terminal

elimination

phase

At

first

urinary

excretion

predominates

and

after

h

faecal

excretion

becomes

the

dominant

route

of

excretion

Discussion

The

present

investigation

was

aimed

at

determining

the

pharmacokinetics

and

excretory

pathways

of

-LSB-

-RSB-

ixabepilone

by

performing

a

mass

balance

study

In

conventional

human

mass

balance

studies

approximately

μCi

of

-LSB-

-RSB-

is

typically

used

to

trace

the

fate

of

a

drug

-LSB-

-RSB-

Due

to

autoradiolysis

of

ixabepilone

this

level

of

labeling

was

not

possible

The

level

of

radioactive

labeling

we

used

was

more

than

lower

at

nCi

The

most

commonly

used

method

for

detection

of

radiotracers

in

mass

balance

studies

is

liquid

scintillation

counting

-LRB-

LSC

-RRB-

This

method

however

relies

on

the

detection

of

β-emissions

and

therefore

can

only

exploit

a

very

small

proportion

of

the

isotope

has

a

half-life

of

years

and

therefore

only

about

of

the

atoms

in

a

sample

decay

over

the

course

of

a

year

AMS

however

is

a

nuclear

physics

technique

that

detects

the

individual

atoms

as

if

they

were

stable

isotopes

and

is

therefore

much

more

sensitive

than

LSC

-LSB-

-RSB-

Originally

AMS

technology

was

developed

in

the

for

radiocarbon

dating

but

has

recently

found

novel

uses

in

biomedical

research

It

has

been

used

to

study

DNA

adducts

of

carcinogens

and

it

can

replace

decay

counting

as

a

method

of

analysis

in

biological

samples

-LSB-

-RSB-

A

first

human

mass

balance

using

this

ultra-sensitive

technique

has

already

been

reported

and

is

expected

to

be

followed

by

many

others

-LSB-

-RSB-

The

ixabepilone

plasma

pharmacokinetic

parameters

observed

in

the

present

investigation

are

similar

to

the

values

previously

reported

for

a

standard

phase

I

dose

escalation

study

in

which

patients

were

administered

of

ixabepilone

in

an

expansion

of

the

recommended

phase

II

dose

-LSB-

-RSB-

However

in

our

study

the

coefficient

of

variation

for

AUCinf

and

Cl

of

ixabepilone

was

and

as

compared

to

and

in

the

phase

I

dose

escalation

study

The

lower

inter-patient

variability

may

result

from

the

greater

rigor

toward

sample

collection

and

processing

that

is

possible

in

a

mass

balance

study

during

which

the

patient

is

hospitalized

It

should

also

be

noted

that

the

administration

of

ixabepilone

as

a

flat

mg

dose

in

the

present

study

did

not

result

in

any

increase

in

inter-patient

variability

compared

with

the

dose

based

on

body

surface

area

which

was

administered

during

the

phase

I

study

Our

results

show

that

ixabepilone

is

extensively

metabolised

This

is

indicated

by

the

plasma

AUC

ratio

of

and

confirmed

by

the

recovery

of

ixabepilone

relative

to

TRA

in

urine

of

approximately

Patient

experienced

a

blocked

bile

duct

resulting

in

a

higher

plasma

TRA

Cmax

and

AUC

but

interestingly

unchanged

ixabepilone

plasma

pharmacokinetics

were

not

affected

and

excretion

of

ixabepilone

metabolites

was

re-routed

to

urine

The

calculated

half-life

of

TRA

was

longer

than

that

of

ixabepilone

-LRB-

of

and

h

respectively

-RRB-

however

we

do

not

conclude

that

TRA

was

eliminated

more

slowly

than

ixabepilone

Comparison

of

ixabepilone

and

TRA

half-lives

per

patient

revealed

that

in

cases

-LRB-

patient

and

-RRB-

the

TRA

half-life

was

shorter

than

the

ixabepilone

half-life

The

mean

TRA

half-life

was

disproportionally

influenced

by

the

long

half-life

observed

in

patient

-LRB-

h

-RRB-

The

very

long

half-life

of

TRA

in

this

patient

is

not

likely

to

be

clinically

relevant

because

this

patient

excreted

of

the

dose

within

days

Based

on

the

half-lives

for

plasma

radioactivity

observed

in

the

other

patients

in

the

once

every

weeks

administration

schedule

accumulation

of

metabolites

should

not

occur

The

seemingly

long

ixabepilone

half-life

of

over

h

is

not

unusual

when

compared

to

other

tubulin-interacting

drugs

Half-lives

of

e.g.

vinca-alkaloids

range

from

h

for

vindesine

and

up

to

a

half-life

of

several

days

for

vincristine

With

an

average

recovery

of

of

the

drug

excreted

over

the

period

the

recovery

of

radioactivity

of

this

mass

balance

study

is

reasonably

good

-LSB-

-RSB-

The

incomplete

recovery

is

explained

by

the

still

ongoing

excretion

at

the

end

of

the

day

collection

period

and

the

long

plasma

half-life

of

TRA

Immediate

assessment

of

the

still

appreciable

amounts

of

radioactivity

excreted

on

day

to

possible

extend

the

period

of

collecting

excreta

as

suggested

in

the

literature

-LSB-

-RSB-

was

not

possible

The

shipping

and

lag-time

in

quantitating

radioactivity

by

AMS

precluded

this

Another

contributing

route

of

elimination

not

monitored

in

the

current

study

is

loss

of

radioactivity

through

expiration

of

-LSB-

-RSB-

At

of

the

dose

versus

faecal

excretion

is

a

quantitatively

more

important

route

of

elimination

than

urinary

excretion

Biliary

excretion

is

governed

by

a

molecular

weight

limit

In

humans

polar

compounds

with

a

molecular

weight

above

approximately

g/mol

are

predominantly

excreted

via

bile

-LSB-

-RSB-

Ixabepilone

metabolites

will

probably

be

more

polar

-LRB-

phase

I

metabolism

oxidation

hydrolysis

etc.

-RRB-

and

have

higher

masses

-LRB-

conjugates

or

phase

II

metabolites

-RRB-

than

ixabepilone

-LRB-

Mwt

g/mol

and

rather

hydrophobic

-RRB-

Whether

this

is

the

case

for

ixabepilone

remains

to

be

investigated

by

metabolic

profiling

of

the

excreta

Given

the

normal

ixabepilone

plasma

concentrations

of

patient

while

experiencing

a

blocked

bile

duct

biliary

excretion

of

unchanged

ixabepilone

into

faeces

may

not

be

a

very

important

elimination

route

and

the

results

suggest

that

ixabepilone

was

equally

well

metabolised

but

that

the

biliary

excretion

of

these

metabolites

was

hindered

by

the

blocked

bile

duct

stent

resulting

in

a

shift

to

urinary

excretion

of

total

radioactivity

The

importance

of

metabolism

in

the

elimination

of

ixabepilone

has

been

confirmed

by

this

study

as

apparent

from

the

low

contribution

of

unchanged

ixabepilone

to

TRA

in

plasma

and

urine

Ixabepilone

related

radioactivity

is

predominantly

excreted

in

the

faeces

Future

investigations

must

be

aimed

at

elucidating

the

metabolic

fate

of

ixabepilone

and

determining

the

activity

of

the

metabolites

Subsequent

identification

of

drug

metabolizing

enzymes

involved

in

ixabepilone

metabolism

may

result

in

explaining

pharmacokinetic

variability

of

ixabepilone

in

individual

patients

O B I O O O O O O B O B I I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O B O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O B I O O B O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O B O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B I O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O B O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B I O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O B O O O O O O O O B O O O O

ixabepilone
epothilone
mass balance
accelerator mass spectrometry


IMGT , the international ImMunoGeneTics information system ® : a standardized approach for immunogenetics and immunoinformatics IMGT , the international ImMunoGeneTics information system ® , was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire -LRB- LIGM -RRB- -LRB- Université Montpellier II and CNRS -RRB- at Montpellier , France . IMGT is a high quality integrated knowledge resource specialized in immunoglobulins -LRB- IG -RRB- , T cell receptors -LRB- TR -RRB- , major histocompatibility complex -LRB- MHC -RRB- of human and other vertebrates , and related proteins of the immune system -LRB- RPI -RRB- of any species which belong to the immunoglobulin superfamily -LRB- IgSF -RRB- and to the MHC superfamily -LRB- MhcSF -RRB- . IMGT consists of five databases , ten on-line tools and more than 8,000 HTML pages of Web resources . IMGT provides a common access to standardized data from genome , genetics , proteome and three-dimensional structures . The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY , a semantic specification of terms to be used in immunogenetics and immunoinformatics . IMGT-ONTOLOGY comprises six main concepts : IDENTIFICATION , CLASSIFICATION , DESCRIPTION , NUMEROTATION , ORIENTATION and OBTENTION . Based on these concepts , the controlled vocabulary and the annotation rules necessary for the immunogenetics data identification , classification , description and numbering and for the management of IMGT knowledge are defined in the IMGT Scientific chart . IMGT is the international reference in immunogenetics and immunoinformatics for medical research -LRB- repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases , AIDS , leukemias , lymphomas , myelomas -RRB- , veterinary research -LRB- IG and TR repertoires in farm and wild life species -RRB- , genome diversity and genome evolution studies of the adaptive immune responses , biotechnology related to antibody engineering -LRB- single chain Fragment variable -LRB- scFv -RRB- , phage displays , combinatorial libraries , chimeric , humanized and human antibodies -RRB- , diagnostics -LRB- detection and follow up of residual diseases -RRB- and therapeutical approaches -LRB- grafts , immunotherapy , vaccinology -RRB- . IMGT is freely available at . Introduction IMGT , the international ImMunoGeneTics information system ® -LSB- 1,2 -RSB- , was created in 1989 , by Marie-Paule Lefranc , at the Laboratoire d'ImmunoGénétique Moléculaire -LRB- LIGM -RRB- -LRB- Université Montpellier II and CNRS -RRB- at Montpellier , France , in order to standardize and manage the complexity of the immunogenetics data . Fifteen years later , IMGT is the international reference in immunogenetics and immunoinformatics , and provides a high quality integrated knowledge resource , specialized in the immunoglobulins -LRB- IG -RRB- and T cell receptors -LRB- TR -RRB- , major histocompatibility complex -LRB- MHC -RRB- of human and other vertebrates , and related proteins of the immune systems -LRB- RPI -RRB- of any species which belong to the immunoglobulin superfamily -LRB- IgSF -RRB- and to the MHC superfamily -LRB- MhcSF -RRB- -LSB- 3-13 -RSB- . The number of potential protein forms of the antigen receptors , IG and TR , is almost unlimited . The potential repertoire of each individual is estimated to comprise about 1012 different IG -LRB- or antibodies -RRB- and TR , and the limiting factor is only the number of B and T cells that an organism is genetically programmed to produce . This huge diversity is inherent to the particularly complex and unique molecular synthesis and genetics of the antigen receptor chains . This includes biological mechanisms such as DNA molecular rearrangements in multiple loci -LRB- three for IG and four for TR in humans -RRB- located on different chromosomes -LRB- four in humans -RRB- , nucleotide deletions and insertions at the rearrangement junctions -LRB- or N-diversity -RRB- , and somatic hypermutations in the IG loci -LRB- see FactsBooks -LSB- 3,4 -RSB- for review -RRB- . Although IMGT was initially implemented for the IG , TR and MHC of human and other vertebrates -LSB- 6 -RSB- , data and knowledge management standardization , based on the IMGT unique numbering -LSB- 14-19 -RSB- , has now been extended to the IgSF -LSB- 15-17,20-22 -RSB- and MhcSF -LSB- 18,23,24 -RSB- of any species . Thus , standardization in IMGT contributed to data enhancement of the system and new expertised data concepts were readily incorporated . IMGT , the international ImMunoGeneTics information system ® consists of five databases , ten on-line tools and Web resources -LSB- 1,2 -RSB- . Databases include sequence databases -LRB- IMGT/LIGM-DB , IMGT/PRIMER-DB and IMGT/MHC-DB -RRB- , one genome database -LRB- IMGT/GENE-DB -RRB- and one three-dimensional -LRB- 3D -RRB- structure database -LRB- IMGT/3Dstructure-DB -RRB- -LSB- 1,2 -RSB- -LRB- Figure 1 -RRB- . Interactive tools are provided for sequence analysis -LRB- IMGT/V-QUEST , IMGT/JunctionAnalysis , IMGT/Allele-Align , IMGT/PhyloGene -RRB- , genome analysis -LRB- IMGT/LocusView , IMGT/GeneView , IMGT/GeneSearch , IMGT/CloneSearch and IMGT/GeneInfo -RRB- and 3D structure analysis -LRB- IMGT/StructuralQuery -RRB- -LSB- 1,2 -RSB- -LRB- Figure 1 -RRB- . Web resources -LRB- `` IMGT Marie-Paule page '' -RRB- comprise more than 8,000 HTML pages of synthesis -LSB- IMGT Repertoire -LRB- for IG and TR , MHC , RPI -RRB- -RSB- , knowledge -LSB- IMGT Scientific chart , IMGT Education -LRB- IMGT Lexique , Aide-mémoire , Tutorials , Questions and answers -RRB- , IMGT Medical page , IMGT Veterinary page , IMGT Biotechnology page , IMGT Index -RSB- , and external links -LSB- IMGT Immunoinformatics page , IMGT Bloc-notes -LRB- Interesting links , etc. -RRB- and IMGT other accesses -LRB- SRS , BLAST , etc. -RRB- -RSB- -LSB- 2 -RSB- . Despite the heterogeneity of these different components , all data in the IMGT information system are expertly annotated . The accuracy , the consistency and the integration of the IMGT data , as well as the coherence between the different IMGT components -LRB- databases , tools and Web resources -RRB- are based on IMGT-ONTOLOGY -LSB- 5 -RSB- , which provides a semantic specification of the terms to be used in immunogenetics and immunoinformatics . IMGT-ONTOLOGY , the first ontology in the domain , has allowed the management of knowledge in immunogenetics -LSB- 2,25 -RSB- and provided standardization for immunogenetics data from genome , genetics , proteome and 3D structures -LSB- 3-13 -RSB- . IMGT-ONTOLOGY concepts are available , for the biologists and IMGT users , in the IMGT Scientific chart -LSB- 2 -RSB- , and for the computing scientists , in IMGT-ML which uses XML -LRB- eXtensible Markup Language -RRB- Schema -LSB- 26 -RSB- . Figure 1 IMGT , the international ImMunoGeneTics information system ® . Databases and tools for sequences , genes and structures are in green , yellow and blue , respectively . The IMGT Repertoire and other Web resources are not shown . Interactions in the genetics , genomics and structural approaches are represented with dotted , continuous and broken lines , respectively . IMGT-ONTOLOGY concepts and IMGT Scientific chart rules The IMGT Scientific chart -LSB- 2 -RSB- comprises the controlled vocabulary and the annotation rules necessary for the immunogenetics data identification , description , classification and numbering and for knowledge management in the IMGT information system . Standardized keywords , labels and annotation rules , standardized IG and TR gene nomenclature , the IMGT unique numbering , and standardized origin/methodology were defined , respectively , based on the six main concepts of IMGT-ONTOLOGY : IDENTIFICATION , CLASSIFICATION , DESCRIPTION , NUMEROTATION , ORIENTATION and OBTENTION -LSB- 2,5 -RSB- -LRB- Table 1 -RRB- . The IMGT Scientific chart is available as a section of the IMGT Web resources -LRB- IMGT Marie-Paule page -RRB- . Examples of IMGT expertised data concepts derived from the IMGT Scientific chart rules are shown in Table 1 . Table 1 IMGT-ONTOLOGY concepts , IMGT Scientific chart rules and examples of IMGT expertised data concepts . IMGT-ONTOLOGY main concepts 5 IMGT Scientific chart rules -LSB- 2 -RSB- Examples of IMGT expertised data concepts -LSB- 2 -RSB- IDENTIFICATION Standardized keywords -LSB- 5 -RSB- Species , molecule type , receptor type , chain type , gene type , structure , functionality , specificity CLASSIFICATION Reference sequencesStandardized IG and TR gene nomenclature -LRB- group , subgroup , gene , allele -RRB- -LSB- 5 -RSB- Nomenclature of the human IG and TR genes -LRB- entry in 1999 in GDB , HGNC -LSB- 27 -RSB- and LocusLink at NCBI -RRB- -LSB- 3 , 4 -RSB- Alignment of alleles -LSB- 3 , 4 -RSB- Nomenclature of the IG and TR genes of all vertebrate species DESCRIPTION Standardized labels and annotations -LSB- 5 -RSB- Core -LRB- V - , D - , J - , C-REGION -RRB- Prototypes -LSB- 5 -RSB- Labels for sequencesLabels for 2D and 3D structures NUMEROTATION IMGT unique numbering -LSB- 14-18 -RSB- for : V - and V-LIKE-DOMAINs -LSB- 16 -RSB- C - and C-LIKE-DOMAINs -LSB- 17 -RSB- G - and G-LIKE-DOMAINs -LSB- 18 -RSB- Protein displaysIMGT Colliers de Perles -LSB- 19 -RSB- FR-IMGT and CDR-IMGT delimitations -LSB- 16 -RSB- Structural loops and beta strands delimitations -LSB- 16 , 17 -RSB- ORIENTATION Orientation of genomic instances relative to each other Chromosome orientation Locus orientation Gene orientation DNA strand orientation OBTENTION Standardized originStandardized methodology -LSB- 2 -RSB- The IMGT Scientific chart rules , based on the IMGT-ONTOLOGY concepts -LSB- 5 -RSB- , are used in the three major IMGT biological approaches , genomics , genetics and structural approaches -LSB- 2 -RSB- , and corresponding data -LRB- Genes , Sequences , 3D structures -RRB- are available in the IMGT components -LRB- databases , tools and Web resources -RRB- -LSB- 1,7-13 -RSB- . IMGT sequence databases , tools and Web resources IMGT sequence databases , tools and Web resources correspond to the IMGT genetics approach that refers to the study of genes in relation with their polymorphisms , mutations , expression , specificity and evolution -LRB- Table 2 -RRB- . The IMGT sequence knowledge management and the IMGT genetics approach heavily rely on the DESCRIPTION concept -LRB- and particularly on the V-REGION , D-REGION , J-REGION and C-REGION core concepts for the IG and TR -RRB- , on the CLASSIFICATION concept -LRB- gene and allele concepts -RRB- and on the NUMEROTATION concept -LRB- IMGT unique numbering -LSB- 14-18 -RSB- -RRB- . Table 2 The IMGT sequence databases , sequence analysis tools and Web resources IMGT sequence databases -LSB- 1 -RSB- IMGT sequence analysis tools -LSB- 1 -RSB- IMGT Repertoire `` Proteins and alleles '' section -LSB- 2 -RSB- -LRB- 2 -RRB- IMGT/LIGM-DB -LSB- 7 -RSB- IMGT/PRIMER-DB -LSB- 1 -RSB- IMGT/MHC-DB -LSB- 28 -RSB- IMGT/V-QUEST -LSB- 10 -RSB- IMGT/JunctionAnalysis -LSB- 11 -RSB- IMGT/Allele-AlignIMGT/PhyloGene -LSB- 12 -RSB- IMGT/Automat -LSB- 29 , 30 -RSB- -LRB- 1 -RRB- Alignments of alleles IG and TR -LSB- 3 , 4 -RSB- Alignments of alleles RPI -LSB- 22 -RSB- Protein displays IG and TR -LSB- 3 , 4 , 16 , 17 -RSB- Protein displays MHC -LSB- 18 -RSB- Protein displays RPI -LSB- 16-18 , 21 -RSB- Tables of alleles IG and TRTables of alleles RPI -LSB- 22 , 24 -RSB- Allotypes Isotypes , etc. -LRB- 1 -RRB- IMGT/Automat -LSB- 29 , 30 -RSB- is an integrated internal IMGT Java tool which automatically performs the annotation of rearranged cDNA sequences that represent the half of the IMGT/LIGM-DB content . So far 7,418 human and mouse IG and TR cDNA sequences have been automatically annotated by the IMGT/Automat tool , with annotations being as reliable and accurate as those provided by a human annotator . -LRB- 2 -RRB- IMGT publications from the IMGT Repertoire `` Proteins and alleles '' section are available as pdf in IMGT Locus in Focus , in IMGT Index -LRB- see also -LSB- 2 -RSB- -RRB- . IMGT sequence databases IMGT/LIGM-DB IMGT/LIGM-DB is the comprehensive IMGT database of IG and TR nucleotide sequences from human and other vertebrate species , with translation for fully annotated sequences -LSB- 7 -RSB- . It was created in 1989 by LIGM -LRB- Montpellier , France -RRB- , and is on the Web since July 1995 -LSB- 6 -RSB- . In August 2005 , IMGT/LIGM-DB contained more than 96,500 sequences of 150 vertebrate species -LSB- 7 -RSB- . The unique source of data for IMGT/LIGM-DB is EMBL , which shares data with the other two generalist databases GenBank and DNA DataBank of Japan -LRB- DDBJ -RRB- . Based on expert analysis , specific detailed annotations are added to IMGT flat files . The annotation procedure includes the IDENTIFICATION of the sequences , the CLASSIFICATION of the IG and TR genes and alleles , and the DESCRIPTION of all IG and TR specific and constitutive motifs within the nucleotide sequences . The Web interface allows searches according to immunogenetic specific criteria and is easy to use without any knowledge in a computing language . Selection is displayed at the top of the resulting sequences pages , so the users can check their own queries . Users have the possibility to modify their request or consult the results with a choice of nine possibilities . The IMGT/LIGM-DB annotations -LRB- gene and allele name assignment , labels -RRB- allow data retrieval not only from IMGT/LIGM-DB , but also from other IMGT databases . Thus , the IMGT/LIGM-DB accession numbers of the cDNA expressed sequences for each human and mouse IG and TR gene are available , with direct links to IMGT/LIGM-DB , in the IMGT/GENE-DB entries . IMGT/LIGM-DB data are also distributed by anonymous FTP servers at CINES and EBI and from many Sequence Retrieval System -LRB- SRS -RRB- sites . IMGT/LIGM-DB can be searched by BLAST or FASTA on different servers -LRB- EBI , IGH , INFOBIOGEN , Institut Pasteur , etc. -RRB- . IMGT/PRIMER-DB IMGT/PRIMER-DB -LSB- 1 -RSB- is the IMGT oligonucleotide primer database for IG and TR , created by LIGM , Montpellier in collaboration with EUROGENTEC S.A. , Belgium , on the Web since February 2002 . In August 2005 , IMGT/PRIMER-DB contained 1,827 entries . IMGT/PRIMER-DB provides standardized information on oligonucleotides -LRB- or Primers -RRB- and combinations of primers -LRB- Sets , Couples -RRB- for IG and TR . These primers are useful for combinatorial library constructions , scFv , phage display or microarray technologies . The IMGT Primer cards are linked to the IMGT/LIGM-DB flat files , IMGT Colliers de Perles and IMGT Alignments of alleles -LRB- IMGT Repertoire -RRB- of the IMGT/LIGM-DB reference sequence used for the primer description . IMGT/MHC-DB IMGT/MHC-DB -LSB- 28 -RSB- comprises databases hosted at EBI and includes a database of human MHC allele sequences or IMGT/MHC-HLA , developed by Cancer Research UK and maintained by ANRI , London , UK , on the Web since December 1998 , and a database of MHC sequences from non human primates IMGT/MHC-NHP , curated by BPRC , The Netherlands , on the Web since April 2002 . IMGT sequence analysis tools The IMGT sequence analysis tools comprise IMGT/V-QUEST -LSB- 10 -RSB- , for the identification of the V , D and J genes and of their mutations , IMGT/JunctionAnalysis -LSB- 11 -RSB- for the analysis of the V-J and V-D-J junctions which confer the antigen receptor specificity , IMGT/Allele-Align for the detection of polymorphisms , and IMGT/PhyloGene -LSB- 12 -RSB- for gene evolution analyses . IMGT/V-QUEST IMGT/V-QUEST -LRB- V-QUEry and STandardization -RRB- is an integrated software for IG and TR -LSB- 10 -RSB- . This tool , easy to use , analyses an input IG or TR germline or rearranged variable nucleotide sequence . The IMGT/V-QUEST results comprise the identification of the V , D and J genes and alleles and the nucleotide alignments by comparison with sequences from the IMGT reference directory , the FR-IMGT and CDR-IMGT delimitations based on the IMGT unique numbering , the translation of the input sequence , the display of nucleotide and amino acid mutations compared to the closest IMGT reference sequence , the identification of the JUNCTION and results from IMGT/JunctionAnalysis -LRB- default option -RRB- , and the two-dimensional -LRB- 2D -RRB- IMGT Collier de Perles representation of the V-REGION -LSB- 10 -RSB- -LRB- `` IMGT/V-QUEST output '' in IMGT/V-QUEST Documentation -RRB- . IMGT/JunctionAnalysis IMGT/JunctionAnalysis -LSB- 11 -RSB- is a tool , complementary to IMGT/V-QUEST , which provides a thorough analysis of the V-J and V-D-J junction of IG and TR rearranged genes . IMGT/JunctionAnalysis identifies the D-GENEs and alleles involved in the IGH , TRB and TRD V-D-J rearrangements by comparison with the IMGT reference directory , and delimits precisely the P , N and D regions -LSB- 11 -RSB- -LRB- `` IMGT/JunctionAnalysis output results '' in IMGT/JunctionAnalysis Documentation -RRB- . Several hundreds of junction sequences can be analysed simultaneously . IMGT/Allele-Align IMGT/Allele-Align is used for the detection of polymorphisms . It allows the comparison of two alleles highlighting the nucleotide and amino acid differences . IMGT/PhyloGene IMGT/PhyloGene -LSB- 12 -RSB- is an easy to use tool for phylogenetic analysis of variable region -LRB- V-REGION -RRB- and constant domain -LRB- C-DOMAIN -RRB- sequences . This tool is particularly useful in developmental and comparative immunology . The users can analyse their own sequences by comparing with the IMGT standardized reference sequences for human and mouse IG and TR -LSB- 12 -RSB- -LRB- IMGT/PhyloGene Documentation -RRB- . IMGT sequence Web resources The IMGT sequence Web resources are compiled in the IMGT Repertoire `` Proteins and alleles '' section that include Alignments of alleles , Proteins displays , Tables of alleles , Allotypes , Isotypes , etc. -LRB- Table 2 -RRB- . Standardized IMGT criteria for amino acid sequence analysis are described in -LSB- 31 -RSB- . IMGT gene databases , tools and Web resources IMGT gene databases , tools and Web resources correspond to the IMGT genomics approach that refers to the studies of the genes within their loci and on their chromosome -LSB- 2 -RSB- -LRB- Table 3 -RRB- . Table 3 The IMGT gene database , genome analysis tools and Web resources IMGT genome database -LSB- 1 -RSB- IMGT genome analysis tools -LSB- 1 -RSB- IMGT Repertoire `` Locus and genes '' section -LSB- 2 -RSB- -LRB- 1 -RRB- IMGT/GENE-DB -LSB- 8 -RSB- IMGT/LocusViewIMGT/GeneViewIMGT / GeneSearchIMGT/CloneSearchIMGT/GeneInfo -LSB- 13 -RSB- Chromosomal localizations -LSB- 3 , 4 -RSB- Locus representations -LSB- 3 , 4 -RSB- Locus descriptionGene exon/intron organizationGene exon/intron splicing sitesGene tablesPotential germline repertoiresLists of genesCorrespondence between nomenclatures -LSB- 3 , 4 -RSB- -LRB- 1 -RRB- IMGT Web resources -LRB- IMGT Marie-Paule page -RRB- also include IMGT Index , IMGT Education -LRB- IMGT Lexique , Aide-mémoire , Tutorials , Questions and answers -RRB- , The IMGT Medical page , The IMGT Veterinary page , The IMGT Biotechnology page , The IMGT Immunoinformatics page , IMGT Bloc-notes -LRB- Interesting links , etc. -RRB- -LSB- 2 -RSB- which are not detailed in this paper . -LRB- 2 -RRB- IMGT publications from the IMGT Repertoire `` Locus and genes '' section are available as pdf in IMGT Locus in Focus , in IMGT Index -LRB- see also -LSB- 2 -RSB- -RRB- . IMGT/GENE-DB , the IMGT gene database Genomic data are managed in IMGT/GENE-DB , which is the comprehensive IMGT genome database -LSB- 8 -RSB- . IMGT/GENE-DB , created by LIGM -LRB- Montpellier , France -RRB- is on the Web since January 2003 . In August 2005 , IMGT/GENE-DB contained 1,377 genes and 2,207 alleles -LRB- 673 IG and TR genes and 1,209 alleles from Homo sapiens , and 704 IG and TR genes and 998 alleles from Mus musculus , Mus cookii , Mus pahari , Mus spretus , Mus saxicola , Mus minutoïdes -RRB- . All the human and mouse IG and TR genes are available in IMGT/GENE-DB . Based on the IMGT CLASSIFICATION concept , all the human IMGT gene names -LSB- 3,4 -RSB- were approved by the Human Genome Organisation -LRB- HUGO -RRB- Nomenclature Committee HGNC in 1999 -LSB- 27 -RSB- , and entered in IMGT/GENE-DB -LSB- 8 -RSB- , Genome DataBase GDB -LRB- Canada -RRB- -LSB- 32 -RSB- , LocusLink and Entrez Gene at NCBI -LRB- USA -RRB- -LSB- 33 -RSB- , and GeneCards -LSB- 34 -RSB- . Reciprocal links exist between IMGT/GENE-DB , and the generalist nomenclature -LRB- HGNC Genew -RRB- and genome databases -LRB- GDB , LocusLink and Entrez at NCBI , and GeneCards -RRB- . All the mouse IG and TR gene names with IMGT reference sequences were provided by IMGT to HGNC and to the Mouse Genome Database -LRB- MGD -RRB- -LSB- 35 -RSB- in July 2002 . Queries in IMGT/GENE-DB can be performed according to IG and TR gene classification criteria and IMGT reference sequences have been defined for each allele of each gene based on one or , whenever possible , several of the following criteria : germline sequence , first sequence published , longest sequence , mapped sequence -LSB- 2 -RSB- . IMGT/GENE-DB interacts dynamically with IMGT/LIGM-DB -LSB- 7 -RSB- to download and display gene-related sequence data . As an example ans as mentioned earlier , the IMGT/GENE-DB entries provide the IMGT/LIGM-DB accession numbers of the IG and TR cDNA sequences which contain a given V , D , J or C gene . This is the first example of an interaction between IMGT databases using the CLASSIFICATION concept . IMGT gene analysis tools The IMGT gene analysis tools comprise IMGT/LocusView , IMGT/GeneView , IMGT/GeneSearch , IMGT/CloneSearch and IMGT/GeneInfo . IMGT/LocusView and IMGT/GeneView manage the locus organization and the gene location and provide the display of physical maps for the human IG , TR and MHC loci and for the mouse TRA/TRD locus . IMGT/LocusView allows to view genes in a locus and to zoom on a given area . IMGT/GeneView allows to view a given gene in a locus . IMGT/GeneSearch allows to search for genes in a locus based on IMGT gene names , functionality or localization on the chromosome . IMGT/CloneSearch provides information on the clones that were used to build the locus contigs displayed in IMGT/LocusView -LRB- accession numbers are from IMGT/LIGM-DB , gene names from IMGT/GENE-DB , and clone position and orientation , and overlapping clones from IMGT/LocusView -RRB- . IMGT/GeneInfo -LSB- 13 -RSB- provides and displays information on the potential TR rearrangements in human and mouse . IMGT gene Web resources The IMGT gene Web resources are compiled in the IMGT Repertoire `` Locus and genes '' section that includes Chromosomal localizations , Locus representations , Locus description , Gene exon/intron organization , Gene exon/intron splicing sites , Gene tables , Potential germline repertoires , the complete lists of human and mouse IG and TR genes , and the correspondences between nomenclatures -LSB- 3,4 -RSB- -LRB- Table 3 -RRB- . The IMGT Repertoire `` Probes and RFLP '' section provides additional data on gene insertion/deletion . IMGT structure database , tool and Web resources The IMGT structural approach refers to the study of the 2D and 3D structures of the IG , TR , MHC and RPI , and to the antigen or ligand binding characteristics in relation with the protein functions , polymorphisms and evolution -LRB- Table 4 -RRB- . The structural approach relies on the CLASSIFICATION concept -LRB- IMGT gene and allele names -RRB- , DESCRIPTION concept -LRB- receptor and chain description , domain delimitations -RRB- , and NUMEROTATION concept -LRB- amino acid positions according to the IMGT unique numbering -LSB- 14-18 -RSB- -RRB- . Table 4 IMGT structure database , analysis tool and Web resources IMGT structural database -LSB- 1 -RSB- IMGT structural analysis tool -LSB- 1 -RSB- IMGT Repertoire `` 2D and 3D structures '' section -LSB- 2 -RSB- IMGT/3D structure-DB -LSB- 15 -RSB- IMGT/StructuralQuery -LSB- 15 -RSB- 2D Colliers de Perles IG and TR -LSB- 3 , 4 , 16 , 17 , 19 -RSB- -LRB- 1 -RRB- 2D Colliers de Perles MHC -LSB- 18 , 36 -RSB- 2D Colliers de Perles RPI -LSB- 16-18 , 21 , 22 , 24 , 37 -RSB- IMGT classes for amino acid characteristics -LSB- 31 -RSB- IMGT Colliers de Perles reference profiles -LSB- 31 -RSB- 3D representations -LRB- 1 -RRB- -LRB- 1 -RRB- Cover of the Nucleic Acids Research 1999 database issue Structural and functional domains of the IG and TR chains comprise the variable domain or V-DOMAIN -LRB- 9-strand beta-sandwich -RRB- which corresponds to the V-J-REGION or V-D-J-REGION and is encoded by two or three genes -LSB- 3,4 -RSB- , the constant domain or C-DOMAIN -LRB- 7-strand beta-sandwich -RRB- , and , for the MHC chains , the groove domain or G-DOMAIN -LRB- 4 beta-strand and one alpha-helix -RRB- . A uniform numbering system for IG and TR V-DOMAINs of all vertebrate species has been established to facilitate sequence comparison and cross-referencing between experiments from different laboratories whatever the antigen receptor -LRB- IG or TR -RRB- , the chain type , or the species -LSB- 14-16 -RSB- . In the IMGT unique numbering , conserved amino acids from frameworks always have the same number whatever the IG or TR variable sequence , and whatever the species they come from . As examples : Cysteine 23 -LRB- in FR1-IMGT -RRB- , Tryptophan 41 -LRB- in FR2-IMGT -RRB- , hydrophobic amino acid 89 and Cysteine 104 -LRB- in FR3-IMGT -RRB- -LRB- Figure 2 -RRB- . This numbering has been applied with success to all the sequences belonging to the V-set of the IgSF -LSB- 20 -RSB- , including non-rearranging sequences in vertebrates -LRB- human CD4 , Xenopus CTXg1 , etc. -RRB- and in invertebrates -LRB- drosophila amalgam , drosophila fasciclin II , etc. -RRB- -LSB- 15,16,21 -RSB- . The IMGT unique numbering , initially defined for the V-DOMAINs of the IG and TR and for the V-LIKE-DOMAINs of IgSF proteins other than IG and TR , has been extended to the C-DOMAINs of the IG and TR -LRB- Figure 2B -RRB- , and to the C-LIKE-DOMAINs of IgSF proteins other than IG and TR -LSB- 17 -RSB- . An IMGT unique numbering has also been implemented for the groove domain -LRB- G-DOMAIN -RRB- of the MHC class I and II chains -LRB- Figure 3 -RRB- , and for the G-LIKE-DOMAINs of MhcSF proteins other than MHC -LSB- 18 -RSB- . Figure 2 IMGT Colliers de Perles of a V-DOMAIN -LRB- A -RRB- and of a C-DOMAIN -LRB- B -RRB- -LRB- code PDB 1mcd in IMGT/3Dstructure-DB -LSB- 9 -RSB- -RRB- . IMGT Colliers de Perles are shown on one layer -LRB- on the left hand side -RRB- and on two layers with hydrogen bonds -LRB- on the right hand side -RRB- . -LRB- A -RRB- The IMGT Collier de Perles of a V-DOMAIN is based on the IMGT unique numbering for V-DOMAIN and V-LIKE-DOMAIN -LSB- 16 -RSB- . The CDR-IMGT are limited by amino acids shown in squares , which belong to the neighbouring FR-IMGT . The CDR3-IMGT extends from position 105 to position 117 . CDR-IMGT regions are colored as follows on the IMGT site : CDR1-IMGT -LRB- blue -RRB- , CDR2-IMGT -LRB- bright green -RRB- , CDR3-IMGT -LRB- dark green -RRB- and hydrogen bonds are shown as green lines . -LRB- B -RRB- The IMGT Collier de Perles of a C-DOMAIN is based on the IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN -LSB- 17 -RSB- . Amino acids are shown in the one-letter abbreviation . Arrows indicate the direction of the beta strands that form the two beta sheets of the immunoglobulin fold -LSB- 3 , 4 -RSB- . Hatched circles correspond to missing positions according to the IMGT unique numbering -LSB- 16 , 17 -RSB- . In the IMGT Collier de Perles on the IMGT Web site hydrophobic amino acids -LRB- hydropathy index with positive value -RRB- and Tryptophan -LRB- W -RRB- found at a given position in more than 50 % of analysed IG and TR sequences are shown in blue , and all Proline -LRB- P -RRB- are shown in yellow . Figure 3 IMGT Colliers de Perles of the two G-DOMAINs of MHC class I -LRB- A -RRB- and of MHC class II -LRB- B -RRB- proteins -LRB- codes PDB 1bd2 and 1aqd , respectively , in IMGT/3Dstructure-DB -LSB- 9 -RSB- -RRB- . The IMGT Collier de Perles of a G-DOMAIN is based on the IMGT unique numbering for G-DOMAIN and G-LIKE-DOMAIN -LSB- 18 -RSB- . -LRB- A -RRB- The two MHC-I G-DOMAINs , G-ALPHA1 -LRB- top -RRB- and G-ALPHA2 -LRB- bottom -RRB- , form the groove of the MHC class I chain -LRB- I-ALPHA -RRB- . -LRB- B -RRB- The two MHC-II G-DOMAINs , G-ALPHA -LRB- top -RRB- of the MHC class II alpha chain -LRB- II-ALPHA -RRB- and G-BETA -LRB- bottom -RRB- of the MHC class II beta chain -LRB- II-BETA -RRB- , form the groove of the MHC class II protein -LSB- 36 -RSB- . Amino acids are shown in the one-letter abbreviation . Hatched circles correspond to missing positions according to the IMGT unique numbering -LSB- 18 -RSB- . Positions in colour correspond to the IMGT contact sites provided , for each peptide/MHC 3D structure , in IMGT/3Dstructure-DB -LSB- 36 -RSB- . IMGT/3Dstructure-DB , the IMGT 3D structure database IMGT/3Dstructure-DB is the IMGT 3D structure database , created by LIGM , and on the Web since November 2001 -LSB- 9 -RSB- . In August 2005 , IMGT/3Dstructure-DB contained 946 atomic coordinate files . IMGT/3Dstructure-DB comprises IG , TR , MHC and RPI with known 3D structures -LSB- 9,36,37 -RSB- . Coordinate files extracted from the Protein Data Bank -LRB- PDB -RRB- -LSB- 38 -RSB- are renumbered according to the standardized IMGT unique numbering -LSB- 16-18 -RSB- . The IMGT/3Dstructure-DB card provides , on-line , the complete information for each IMGT/3Dstructure-DB entry . The IMGT/3Dstructure-DB card shows a summary table and a menu that gives access to five sections : `` Chain details '' , `` Contact analysis '' , `` Visualization with Jmol '' , `` Renumbered file '' and `` References and links '' . The `` Chain details '' section provides chain description , IMGT gene and allele names , IMGT chain and domain labels , domain delimitations , amino acid positions according to the IMGT unique numbering , IMGT Colliers de Perles -LSB- 16-19 -RSB- . The `` Contact analysis '' section provides contact types and categories between domains -LRB- in IMGT/3Dstructure-DB Domain contacts -RRB- and atom contacts at the residue and position level -LRB- in IMGT/3Dstructure-DB Residue@Position contacts -RRB- -LSB- 37 -RSB- . -LRB- IMGT/3Dstructure-DB Documentation -RRB- . The `` Renumbered file '' section downloadable provides renumbered IMGT/3Dstructure-DB flat files . IMGT/StructuralQuery tool The IMGT/StructuralQuery tool -LSB- 9 -RSB- analyses the interactions of the residues of the antigen receptors IG and TR , MHC , RPI , antigens and ligands . The contacts are described per domain -LRB- intra - and inter-domain contacts -RRB- and annotated in term of IMGT labels -LRB- chains , domain -RRB- , positions -LRB- IMGT unique numbering -RRB- , backbone or side-chain implication -LSB- 37 -RSB- . IMGT/StructuralQuery allows to retrieve the IMGT/3Dstructure-DB entries , based on specific structural characteristics : phi and psi angles , accessible surface area -LRB- ASA -RRB- , amino acid type , distance in angstrom between amino acids , CDR-IMGT lengths . IMGT structure Web resources The IMGT stucture Web resources are compiled in the IMGT Repertoire `` 2D and 3D structures '' section which includes 2D representations or IMGT Colliers de Perles -LSB- 16-19 -RSB- , 3D representations , FR-IMGT and CDR-IMGT lengths -LSB- 16 -RSB- , amino acid chemical characteristics profiles -LSB- 31 -RSB- , etc. . In order to appropriately analyse the amino acid resemblances and differences between IG , TR , MHC and RPI chains , eleven IMGT classes were defined for the ` chemical characteristics ' amino acid properties and used to set up IMGT Colliers de Perles reference profiles -LSB- 31 -RSB- . The IMGT Colliers de Perles reference profiles allow to easily compare amino acid properties at each position whatever the domain , the chain , the receptor or the species . The IG and TR variable and constant domains represent a privileged situation for the analysis of amino acid properties in relation with 3D structures , by the conservation of their 3D structure despite divergent amino acid sequences , and by the considerable amount of genomic -LRB- IMGT Repertoire -RRB- , structural -LRB- IMGT/3Dstructure-DB -RRB- and functional data available . These data are not only useful to study mutations and allele polymorphisms , but are also needed to establish correlations between amino acids in the protein sequences and 3D structures and to determine amino acids potentially involved in the immunogenicity . Conclusion In order to allow any IMGT component to be automatically queried and to achieve a higher level of interoperability inside the IMGT information system and with other information systems , our current objectives include the modelling of the three major IMGT biological approaches , genomics , genetics and structural approaches , the analysis of the IMGT components -LRB- databases , tools and Web resources -RRB- in relation with the concepts , and the development of Web services -LSB- 2 -RSB- . They are the first steps towards the implementation of IMGT-Choreography -LSB- 2 -RSB- , which corresponds to the process of complex immunogenetics knowledge -LSB- 25 -RSB- and to the connection of treatments performed by the IMGT component Web services . IMGT-Choreography has for goal to combine and join the IMGT database queries and analysis tools . In order to keep only significant approaches , a rigorous analysis of the scientific standards -LSB- 3,4 -RSB- , of the biologist requests and of the clinician needs -LSB- 39-42 -RSB- has been undertaken in the three main biological approaches : genomics , genetics and structural approaches . The design of IMGT-Choreography and the creation of dynamic interactions between the IMGT databases and tools , using the Web services and IMGT-ML , represent novel and major developments of IMGT , the international reference in immunogenetics and immunoinformatics . IMGT-Choreography enhances the dynamic interactions between the IMGT components to answer complex biological and clinical requests . Since July 1995 , IMGT has been available on the Web at . IMGT has an exceptional response with more than 140,000 requests a month . The information is of much value to clinicians and biological scientists in general . IMGT databases , tools and Web resources are extensively queried and used by scientists from both academic and industrial laboratories , from very diverse research domains : -LRB- i -RRB- fundamental and medical research -LRB- repertoire analysis of the IG antibody sites and of the TR recognition sites in normal and pathological situations such as autoimmune diseases , infectious diseases , AIDS , leukemias , lymphomas , myelomas -RRB- , -LRB- ii -RRB- veterinary research -LRB- IG and TR repertoires in farm and wild life species -RRB- , -LRB- iii -RRB- genome diversity and genome evolution studies of the adaptive immune responses , -LRB- iv -RRB- structural evolution of the IgSF and MhcSF proteins , -LRB- v -RRB- biotechnology related to antibody engineering -LRB- single chain Fragment variable -LRB- scFv -RRB- , phage displays , combinatorial libraries , chimeric , humanized and human antibodies -RRB- , -LRB- vi -RRB- diagnostics -LRB- clonalities , detection and follow up of residual diseases -RRB- and -LRB- vii -RRB- therapeutical approaches -LRB- grafts , immunotherapy , vaccinology -RRB- . Citing IMGT If you use IMGT databases , tools and/or Web resources , please cite -LSB- 1 -RSB- and this paper as references , and quote the IMGT Home page URL address , .

B O O O B B I O O O O O O B O B B O O O B B I O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B I O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O B B O O O O O O B B O O O O B O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O B O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O B O O O O O B O O O B O O O O O B O B O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O B B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O O B O B O O O O O O O B I O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O B B O O O O O O B B O O O O O O O O O O O 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O O O B O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B B I O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O O B B I O O O O O O B O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O B O O O B O O O O O O B O O O O O O B O O O O O O O O O O O O O O B O O O O O O B O O O O O O O O B O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O B O O O O O O O O O B O O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O B O O O O O B O O O O O O O O O B O O O O O O O B B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O B O O O O B O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O B O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B B I I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O B O B O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O B O O B O O B O O O O O O O O O O O O B O O O O B O O O O B O O O O B B O O B O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O B O O O O O B O O O O O O O O O O O O B O B O O O O O O O O O O O B O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O B O O O O O O B O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O B O B O O O O O O B O B O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B B I I O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B B I I O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O B B I I O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B B I I O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O B O O O O O O O B I O O O O O O O O O O B B I B O O O B B I B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O B O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B O O O O O O O O O O O O O O O O O B O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O B B I O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O B O O O O O O O O O O O O O B B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O B O O O O O B O B O O O O O O O O B O O O O O O O O O O O O O B O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O O O O O O O O O O B O O O O O O

imgt
antibody
immunoglobulin
superfamily
mhc
ontology
database
information system
knowledge resource
immunoinformatics
immunogenetics
collier de perles
3d structure
annotation

t cell receptor
hla
three-dimensional
polymorphism