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GDI use jou neys
Index
Aim and scope ............................................................................................................................ 2
Ve sioning ............................................................................................................................... 3
Glossa y .................................................................................................................................. 4
Wo k low ........................................................................................................................................ 5
GDI esea che use jou neys ................................................................................................... 7
Au hen ica e in o GDI Fede a ion .................................................................................................. 7
Da a Disco e y using Use Po al’s Da a Ca alogue o Au hen ica ed Use s ........................... 8
Da a Disco e y using GDI’s Beacon Ne wo k o Au hen ica ed Use s ...................................... 9
Da a Access Reques .................................................................................................................. 10
Posi i e applica ion esponse .................................................................................................... 11
Amend an applica ion ................................................................................................................. 12
Da a Applica ions O e iew ( o g an ed access da a) ............................................................ 13
Fede a ed Da a Compu a ion ..................................................................................................... 14
Download analy ical (and mos ly agg ega ed) esul s ............................................................. 16
Submission o an analy ical wo k low ....................................................................................... 17
Accep ance o an analy ical wo k low ....................................................................................... 18
Denial o an analy ical wo k low ................................................................................................ 19
GDI use s o ies bo n om use jou neys ............................................................................... 21
Enabling con ac wi h ea ing heal hca e p o essional ........................................................... 21
Pa ien s diagnosed wi h me as a ic melanoma ....................................................................... 22
Look up a ian summa y da a in and ac oss GDI da ase s .................................................... 24
Lookup o indi idual gene ic a ian s ........................................................................................ 27
Cance as a Ra e Disease ........................................................................................................... 28
Gene ic a ian isk assessmen wi hin heal hca e .................................................................. 30
Me as a ic Colo ec al Cance .................................................................................................... 31
GWAS analysis ............................................................................................................................ 33
GWAS analyses ac oss ede a ed nodes .................................................................................. 34
Recalib a ion o polygenic isk sco es ...................................................................................... 35
Ances y-speci ic impu a ion ..................................................................................................... 36
Annex .................................................................................................................................... 37
Documen a ion ............................................................................................................................ 37
P oposed GDI Access Wo k low ................................................................................................ 38
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Aim and scope
This documen aims o gi e a high-le el desc ip ion o GDI’s mos common usages and, h ough
hem, p o ide a b oad o e iew o expec ed unc ionali ies and basic equi emen s.
By eading and dissec ing each use jou ney and s o y, he eade can en ision he b icklaying
wo k being done owa ds a pan-Eu opean heal h da a ne wo k in as uc u e, wi h eal examples
o daily esea ch wo k ( anging om a ian sea ch o e la ge popula ions o suppo ing cance
mul imodal ini ia i es) whe e his ne wo k will be no only help ul bu ounda ional.
The GDI use jou ney sec ion desc ibes he speci ic s eps a use will ake when in e ac ing wi h
he GDI. I gi es a high-le el desc ip ion o GDI’s mos common usages and, h ough hem,
p o ides a b oad o e iew o expec ed unc ionali ies and basic equi emen s. The use jou neys
map ou he use ’s expe ience, om he ini ial poin o con ac (i.e. he au hen ica ion in o GDI
Fede a ion) o he inal goal (i.e. da a access and analysis), p o iding con ex and a deepe
unde s anding o he conside a ions and challenges he use aces along he way. These use
jou neys a e designed o be echnology-agnos ic, ocusing on use needs a he han speci ic
implemen a ions. Subsequen ly, use s o ies ha e been de i ed om hese use jou neys,
p o iding p ac ical examples.
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Ve sioning
Da e
M m
Who
Desc ip ion
21/06/2024
1
EGJ (BSC)
Fi s d a , in e nal discussion
20/07/2024
2
CHF (BSC)
Second d a a e discussion wi h WP7 -
Ma co Mo elli’s eam
26/08/2024
3
CHF (BSC)
Ve sion a e discussion wi hin ull Pilla III
30/08/2024
4
LP (BSC)
Include commen s by Pilla I + o he eedback
20/09/2024
5
LP (BSC)
Upda ed numbe ing o s o ies, s o ies names
and upda ed s o ies con en
09/12/2024
6
CHF (BSC)
Added wo new use jou neys om D7.5 use
s o ies
20/01/2025
7
LP, CHF, EGJ
(BSC)
Final e sion o use jou neys o be ozen
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Glossa y
- (Da a) Use . An iden i ied, au hen ica ed eal pe son belonging o a esea ch o heal h
o ganisa ion ha uses GDI in as uc u e. A use has a se ies o conno a ions acco ding
o hei backg ound acco ding o he Heal hyCloud use p o iles and sub-p o iles1, he
1+MG Go e nance and ELSI2, and he 1+MG Glossa y3:
- Resea che s. Resea che s a e hose indi iduals ha will in e ac wi h GDI's
in as uc u e wi h he goal o ob ain, p ocess, and/o analyse esea ch da a and
i s po en ially associa ed ou comes.
- Heal hca e p o essional. A heal hca e p o essional is a pe son ha has an ac i e
ole in p ocessing, analysing and/o unde s anding heal h- ela ed da a. Thei main
goal while using GDI's in as uc u e is o ob ain knowledge ha could be
ans e ed o clinical p ac ice.
- Policy make . I is a pe son, o g oup o people, esponsible o o in ol ed in
o mula ing policies4, especially in poli ics and ela ed o heal hca e. In o de o
ul il hei du ies, hey migh need o access high le el s a is ics o GDI, usage o
GDI’s da a, o GDI’s da a in i s ac ion o comple eness. A use also includes
consul ancies who de elop policies o a policy make .
- Da a p o ide . Acco ding o he de ini ion in Heal hyCloud1, a da a p o ide is a pe son o
en i y ha gene a es and/o makes a ailable heal h- ela ed da a in o he 1+MG, ei he as
a p oduc o hei ac i i y o as manda ed by ano he indi idual o o ganisa ion. The da a
p o ide may no be he one who has collec ed he da a. The da a p o ide does no ac
is-a- is he use bu ans e s he (legal) esponsibili y o he disclosu e o he use o
he Genome EDIC. Then, he 1+MG Go e nance and ELSI2, and he 1+MG Glossa y3
equi es o ex a de ail:
- Da a con olle (can be a join con olle ). Da a con olle s a e hose ha , as a
na u al o legal pe son, as well as a public au ho i y, alone o join ly wi h o he s,
de e mines he pu poses and means o p ocessing GDI’s da a o a subse o i ( o
ins ance he da a in a na ional node). A da a con olle does no equi e o ha e
access o he da a no o hos i o exe cise he ole. In addi ion, a da a con olle
is a quali ica ion unde he GDPR and changes along he da a li e cycle.
- Da a p o ide a e con olle s o b inging da a in o he Genome EDIC
- The Genome EDIC is con olle o he disclosu e o he use
- The use is con olle o he da a use such as a esea ch p ojec
1 FAIR Heal h Da a Po al expec ed use s' in e ac ions: h ps://zenodo.o g/ eco ds/10225882
2 1+MG Go e nance and ELSI: h ps:// amewo k.onemilliongenomes.eu/go e nance-elsi
3 1+MG Glossa y - e sion o 1+MG F amewo k: h ps://zenodo.o g/ eco ds/8279620
4 Heal h Resea che s and Policy Make s: A Need o S eng hen Rela ionship:
h ps://www.ncbi.nlm.nih.go /pmc/a icles/PMC3191660/
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- When we ha e subjec -le el da a disco e y in ad ance o an access
eques , he use and EDIC a e join con olle s o hose ope a ions.
- Da a hos . A na u al o legal pe son, a public au ho i y, o a hi d pa y en i y (such
as Amazon, Mic oso o Google) ha s o es any subse o GDI's da a, usually on
behal o ano he en i y (usually a da a con olle ).
- IT in as uc u e p o ide . I is a legal pe son, as well as public au ho i y, ha con ibu es
o GDI by p o iding physical and/o compu a ional in as uc u e o achie e he p ojec ’s
goals in e ms o da a s o age capabili ies, da a p ocessing capabili ies, and/o logis ic
ope a i e suppo capabili ies o enable mee ing he p ojec ’s long- e m needs.
- Da a p ocesso . Acco ding o he 1+MG Glossa y3, a Da a p ocesso is a na u al
o legal pe son, as well as public au ho i y, which p ocesses pe sonal and/o
heal h da a on behal o he Da a con olle .
- (Da a) P ocessing. Da a p ocessing co e s any so o p ocess (including holding da a)
co e ing he non exhaus ing aspec s o aining AI models, analysis o clinical and/o
gene ic da a o esea ch pu poses, iden i ica ion o sha ed pa hologies ac oss da ase s
(bo h using clinical and/o gene ic da a o do so) o high le el o low le el s a is ics on
da a collec ions, da a se s o indi idual eco ds.
- Da a. Any digi al in o ma ion suscep ible o being used in heal h esea ch and egula ed
by p e iously men ioned laws and s o ed wi hin GDI’s p emises.
- (Indi idual) Reco d. Da a ela ed o indi idual da a subjec s.
- Da a se . Indi idual eco ds ha a e g ouped in a ce ain con ex ( o example:
p ojec ha gene a ed he "da a", clinical condi ion de ini ion, e c.). hey can be
cha ac e ised using non-pe sonal me ada a.
- Da a collec ion. Da a se s ha a e g ouped oge he in a ce ain con ex and
coming om he same da a con olle (s). They can be cha ac e ised wi h non-
pe sonal me ada a. A da a collec ion, o ins ance, e e s o da a o a coho o
public egis y.
- Clinical da a. Pe sonal da a ela ed o he physical o men al heal h o an indi idual
da a subjec independen o i s o igin (e.g. om heal hca e, esea ch, clinical ials
con ex s - among o he s). In 1+MG’s Glossa y his is e e ed o as "heal h da a",
wi h o he g anula i y as "heal hca e da a" and "heal h esea ch da a"; in o he
p ojec s “pheno ypic da a” is also used o desc ibe his in o ma ion and in Beacon
2 i is called “phenoclinic da a”.
- Gene ic da a. Pe sonal da a ela ed o he inhe i ed o acqui ed gene ic
cha ac e is ics o an indi idual which gi e unique in o ma ion abou hei
physiology o heal h, and which esul s om an analysis o a biological sample
om he indi idual ques ion.
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Wo k low
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GDI esea che use jou neys
Au hen ica e in o GDI Fede a ion
#:
ujGdi01
S o y name:
T igge ed by Use Role:
Resea che and/o heal h p o essional
Au ho s and Con ibu o s:
EGJ
P econdi ions:
- Use belongs o a ecognized esea ch o heal h o ganisa ion
- Use ’s na ional node uses a compa ible and con igu ed IAM
Desc ip ion:
Use aims o au hen ica e o any o GDI cen al se ices. The use goes o he selec ed cen al
se ice and is able o, le e aging hei na ional node’s IAM solu ion, log in in o cen al se ices
p ope ly au hen ica ed wi h hei na ional digi al iden i y.
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Da a Disco e y using Use Po al’s Da a Ca alogue o
Au hen ica ed Use s
#:
ujGdi02
S o y name:
Disco e a da ase o in e es o a scien i ic pu pose
T igge ed by Use Role:
Resea che and/o heal h p o essional
Au ho s and Con ibu o s:
ND, LP, EGJ, GC, TP, LW
P econdi ions:
- Da a ca alogue is de ined and included in he GDI Use Po al, displaying he me ada a
o each da ase disco e able. The Da a Ca alogue will p o ide basic and ad anced
que ying and il e ing op ions o he use . Cu en ly he da a ca alogue is open access
as i does no include any pe sonal da a and can be explo ed wi hou logging in.
- The me ada a is g anula enough o help he use iden i y he igh da ase s
- The use unde s ands wha me ada a om GDI’s da ase s is ele an o hei pu pose.
Desc ip ion:
A use aims o disco e da ase s o in e es . The use explo es he Da a Ca alogue and uses
he sea ch and il e unc ionali ies o iden i y he da ase s ha align wi h hei objec i es and
equi emen s.
This sea ch is done based only on me ada a associa ed wi h each da ase , ha me ada a can
be downloaded i he use wishes o do so.
Pos condi ions:
- None
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Da a Disco e y using GDI’s Beacon Ne wo k o
Au hen ica ed Use s
#:
ujGdi03
S o y name:
Disco e a da ase o in e es o a scien i ic pu pose
T igge ed by Use Role:
Resea che
Au ho s and Con ibu o s:
ND, LP, CHF, EGJ
P econdi ions:
- Following ujGdi01
Desc ip ion:
A use aims o disco e da ase s o in e es . They access he GDI’s Use Po al and au hen ica e
ollowing ujGdi01. Once logged in, he use decides o explo e he da a by pe o ming a
Beacon’ clinical and/o genomic que y h ough a sea ch box.
This que y elies on he GDI capabili ies o sea ching o e da ase acco ding o he ac ual
phenoclinic and genomic da a in he da ase s. The esponse ob ained om GDI’s In as uc u e
includes he numbe o indi iduals in each da ase ha mee he p ope ies de ined a he que y
among o he in o ma ion.
Pos condi ions:
- None
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Download analy ical (and mos ly agg ega ed) esul s
#:
ujGdi09
S o y name:
Download analy ical esul s
T igge ed by Use Role:
Resea che and/o heal h p o essional
Au ho s and Con ibu o s:
EGJ, CHF
P econdi ions:
- The use has execu ed an analysis ollowing ujGdi08.
- The use has been g an ed access o he esul s o he analysis execu ed (all nodes had
e oed he esul s).
- All nodes can connec he o he nodes wi h he pu pose o accessing he esul s o ha
use execu ions hey ha e s o ed.
The analy ical wo k low he use selec ed is composed by wo sec ions: 1) a se ies o asks
ha mus be un in mul iple na ional nodes o ex ac key in o ma ion om he da ase s o
in e es by he esea che , o gene a e in e media e esul s (ujGdi08); 2) an ex a s ep ha will
agg ega e he esul s om he p e ious s ep in a single “ inal esul ” (ujGdi08).
The e will be scena ios whe e he second s ep is no necessa y and wha is called “pa ial inal
esul s” a e, in ac , he “ inal esul s” (one in each o he in ol ed na ional nodes).
To he use , i is key o be able o download bo h he “pa ial inal esul s” and he “ inal esul ”
o he selec ed analy ical wo k low in o de o pu sue hei esea ch.
The na ional node he esea che belongs o will be he one in cha ge o collec he “pa ial inal
esul s”. I he second s ep (agg ega ion) is necessa y, i will also be esponsible o make he
agg ega ion ( o example, he me a analysis done om mul iple GWAS analysis). Then, bo h
he “pa ial inal esul s” and he “ inal esul ” should be accessible om he use ’s node.
Pos condi ions:
- Bo h “pa ial inal esul s” and “ inal esul s” a e accessible by he use a he end o
ujGdi08 + ujGdi09 ( his use jou ney).
- O he nodes in ol ed in ujGdi08 a e allowed o dele e empo a y esul s a e some
ime o ujGdi08
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Submission o an analy ical wo k low
#:
ujGdi10
S o y name:
Submission o an analy ical wo k low
T igge ed by Use Role:
Au ho s and Con ibu o s:
EGJ, CHF
P econdi ions
- The use au hen ica es hemsel es in GDI ollowing ujGdi01
- The use unde s ands GDI’s Fede a ed Compu a ion Dashboa d ea u es and how o
de ine an analy ical wo k low.
Desc ip ion
The use has an idea o an analy ical wo k low in o de o answe hei scien i ic ques ions, o
which hey wan o use he GDI in as uc u e and da a esou ces.
In o de o do so, he use inspec s he Ma ke place, whe e all he applica ions (so wa e and
models) eside. Picking om he lis and conca ena ing he di e en applica ions, he use is
able o c ea e a new analy ical wo k low, ei he using a g aphical use in e ace applica ion such
as he Fede a ed Compu a ion Dashboa d o using a wo k low desc ip ion language.
Once he use has he analy ical wo k low de ined, hey can submi i o accep ance in o GDI
using he same Fede a ed Compu a ion Dashboa d. GDI will answe he use in a easonable
amoun o ime. Du ing his ime GDI will: A) check ha he analy ical wo k low does no leak
any da a no pe o ms any undesi ed ope a ion, and B) in o m he na ional nodes abou he new
wo k low, which will ha e some ime (wi hin he o iginal easonable amoun o ime) o es he
wo k low and aise any echnical issues in which case hey can eques changes be made o
he wo k low and he applica ion o begin anew. I bo h A and B a e success ul, ujGdi11.
O he wise ujGdi12.
Pos condi ions
- The analy ical wo k low is submi ed in o GDI’s sys em and accessible by GDI’s s a
and na ional nodes o i s alida ion.
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Accep ance o an analy ical wo k low
#:
ujGdi11
S o y name:
Accep ance o an analy ical wo k low
T igge ed by Use Role:
Technical pe sonal om na ional SPE
Au ho s and Con ibu o s:
EGJ, CHF
P econdi ions
- The use au hen ica es hemsel es in GDI ollowing ujGdi01.
- The use has submi ed an analy ical wo k low o alida ion.
Desc ip ion
The GDI alida ion commi ee ecei es a no i ica ion om GDI’s Fede a ion Commu a ion
Dashboa d indica ing ha an analy ical wo k low has been submi ed o alida ions.
The commi ee inspec s he mul iple asks o he wo k low o ensu e no da a is leaked du ing
i s execu ion and ha all he ope a ions pe o med a e pe mea ed in he p ojec .
Seeing ha all he asks a e co ec , he commi ee no i ies he na ional nodes o local es ing.
The na ional nodes will be gi en a easonable amoun o ime o locally es he wo k low i
desi ed. A e ha amoun o ime expi es o i hey submi a posi i e esul , he analy ical
wo k low will be lagged as accep able.
The alida ion commi ee will collec all he eedback om he na ional nodes and, inding hem
all (ac i ely o passi ely) posi i e, hey lag he analy ical wo k low as accep ed. Doing so, he
GDI’s Fede a ed Compu a ional Dashboa d will now include he analy ical wo k low as usable
by GDI’s use and will no i y he owne o he posi i e alida ion esul s.
Pos condi ions
- The analy ical wo k low is now lis ed as usable wi hin GDI ede a ed compu a ion
in as uc u e.
- The use ha submi ed he wo k low is no i ied o he posi i e esul s.
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Denial o an analy ical wo k low
#:
ujGdi12
S o y name:
Deny o an analy ical wo k low
T igge ed by Use Role:
Technical pe sonal om na ional SPE
Au ho s and Con ibu o s:
EGJ, CHF
P econdi ions
- The use au hen ica es hemsel es in GDI ollowing ujGdi01.
- The use has submi ed an analy ical wo k low o alida ion.
Desc ip ion
The GDI alida ion commi ee ecei es a no i ica ion om GDI’s Fede a ion Commu a ion
Dashboa d indica ing ha an analy ical wo k low has been submi ed o alida ions.
The commi ee inspec s he mul iple asks o he wo k low o ensu e no da a is leaked du ing
i s execu ion and ha all he ope a ions pe o med a e pe mea ed in he p ojec .
I he commi ee iden i ies a possible da a leak o ha some o he ope a ions pe o med by
he analy ical wo k lows a e unaccep able wi hin GDI’s con ex , hey lag he analy ical
wo k low as ejec ed (indica ing which ope a ions a e leaking da a and/o which ope a ions a e
no accep ed).
I he commi ee sees ha all he asks a e co ec , he commi ee hen no i ies he na ional
nodes o local es ing. The na ional nodes will be gi en a easonable amoun o ime o locally
es he wo k low i desi ed.
Du ing ha ime he na ional nodes can es he analy ical wo k low. I hey iden i y echnical
o legal issues ha o bids hem o un he wo k low locally, hey will documen he issue and
ag he wo k low as unaccep able.
Ei he because he alida ion commi ee lagged he analy ical wo k low as unaccep able o
because some na ional node epo ed issues, he wo k low is epo ed no o be accep ed in
GDI’s sys em. In doing so, he GDI’s Fede a ed Compu a ional Dashboa d will no i y he owne
o he nega i e alida ion, p o iding use ul eedback ha can be used o ix he epo ed issues.
The wo k low hen could be submi ed again o GDI’s ne wo k.
Pos condi ions
- The analy ical wo k low was no included in GDI’s sys em.
- The use ha submi ed he wo k low is no i ied o he nega i e esul s and use ul
eedback is p o ided in o de o c ea e a new analy ical wo k low wi h he same
unc ionali y bu ha has highe possibili ies o be accep ed in GDI.
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GDI use s o ies bo n om use jou neys
Enabling con ac wi h ea ing heal hca e p o essional
#:
usGdi01
S o y name:
The use wan s o se up a communica ion channel wi h he
ele an clinical con ac ela ed o pa ien s wi h he same
gene ic and/o clinical condi ion as hei s o discuss possible
ou comes
T igge ed by Use Role:
Heal h p o essional
Au ho s and Con ibu o s:
MM, EB, GG, FC, LP, CHF, GC, TB
P econdi ion:
- The use mus be au hen ica ed, au ho ised, and alid o GDI.
- Doing a que y cons i u es a “da a p ocessing” ac i i y; he e o e, he
o ganisa ion whe e he use belongs needs o ha e a da a-use ag eemen wi h
Genome-EDIC.
Desc ip ion:
A use has an indi idual case wi h a pa icula gene ic and/o clinical desc ip ion. In o de o
p oceed wi h cau ion, hey wan o con ac o he heal hca e p o essionals ha deal wi h simila
cases.
The use will ollow he p ocess desc ibed in “Lookup o indi idual gene ic a ian s”
(usGdi02.1) o iden i y da ase s con aining simila indi iduals o he one o hei in e es .
The use goes back o he ele an communica ion channel in he Use Po al and desc ibes
hei case-in-ques ion (p o iding he ids o da ase s o in e es ) and submi s i , expec ing a
no i ica ion when he communica ion channel be ween hem is a ailable in a speci ied ime
ame.
Pos condi ions:
- The use ends up ha ing he ele an con ac o hei speci ic case media ed h ough
he Use Po al (aka, ele an communica ion channel).
- Al hough included in he da a-use ag eemen , he use will no , unde any se ing,
con ac any pa ien disco e ed using his use s o y.
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Pa ien s diagnosed wi h me as a ic melanoma
#:
usGdi01.1
S o y name:
Enabling con ac wi h ea ing heal hca e p o essional o a
pa ien diagnosed wi h me as a ic melanoma
T igge ed by Use Role:
Clinician/oncologis
Au ho s and Con ibu o s:
F om D7.5 - Cance Resea ch use case
Use s o y desc ip ion:
The use case is a e inemen o usGdi01 (Enabling con ac wi h ea ing heal hca e
p o essionals o discuss possible ou comes ela ed o pa ien s wi h simila gene ic o clinical
condi ions) o a eal case scena io.
A clinician needs o ind a second he apeu ic op ion o his/he pa ien diagnosed wi h
me as a ic melanoma, jus i ied by he iden i ica ion o possible a ge able mu a ion(s). A
seconda y objec i e is o ind he molecula al e a ions explaining he eme gence o he
esis ance o he p ima y cance ea men .
The goal is o ind a simila case in he GDI da abases, by que ying he ne wo k, i.e. ind
melanoma pa ien s wi h a BRAF poin mu a ion, ea ed wi h BRAF inhibi o Vemu a enib, who
ha e a mu a ion in he PTEN gene (known a ian esponsible o he apy esis ance). The goal
is o sea ch o exis ing in o ma ion on he PTEN gene, he BRAF mu a ion and he impac o
he mu a ion on he Kinase pa hway ha can explain d ug esis ance in melanoma cance
pa ien s.
P econdi ions:
The clinician mus be au hen ica ed and au ho ised o GDI.
Desc ip ion:
● The clinician logs in o he GDI pla o m (ujGdi01) and b owses a ailable da ase s
(ujGdi02 o ujGdi03).
● The clinician inpu s a Beacon que y (ujGdi03) using genomic coo dina es o gene
usion e ms, o ind pa ien s wi h a PTEN dele ion in he genomic da a. Da a a e il e ed
o ocus on he mos ele an cases: pa ien s wi h melanoma and wi h de ails
conce ning he cha ac e is ics o he pa ien , he esponses o he ea men , and
su i al a es.
● The GDI e u ns esul s, which may include a da ase ela i e o ano he pa ien wi h a
simila disease and he apy his o y, ound on one node o he ne wo k. The da ase is
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#:
usGdi01.1
S o y name:
Enabling con ac wi h ea ing heal hca e p o essional o a
pa ien diagnosed wi h me as a ic melanoma
T igge ed by Use Role:
Clinician/oncologis
Au ho s and Con ibu o s:
F om D7.5 - Cance Resea ch use case
composed o gene ic da a (NGS sequencing o a melanoma ea ed wi h Vemu a enib,
a e de eloping esis ance o he he apy) and he co esponding clinical da a. Bo h
aw gene ic da a (.Fas q ile) and analysed da a (. c ile con aining soma ic mu a ions
and BED ile con aining s uc u al al e a ions) a e p esen . Agg ega ed da a could be
isualised ia a isualisa ion ool like in cBiopo al.
● I needed, a communica ion channel wi h he ele an clinical con ac ela ed o he
iden i ied pa ien (s) can be se up.
● The clinician applies o da a access o 1+MG da a (ujGdi04) and he Da a Access
Commi ee g an s he access (ujGdi05).
● The clinician downloads he gene ic sequence da a wi h he co esponding clinical da a
o he iden i ied pa ien (s) (ujGdi09).
Pos condi ions:
-
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Look up a ian summa y da a in and ac oss GDI da ase s
#:
usGdi02
S o y name:
Look up a ian summa y da a in and ac oss GDI da ase s
T igge ed by Use Role:
Resea che and/o heal h p o essional
Au ho s and Con ibu o s:
LW, GC, TP, CHF
Use s o y desc ip ion:
“As a [clinician/ esea che /policy make ], I would like o look up he equency o a gi en allele
in a gi en [disease, disease ype, popula ion, ances y...] in o de o [in e oga e pa hogenici y
o he allele/in e he e icacy o a known d ug using pha macogenomics knowledge/...]”
P econdi ions:
- A da abase con aining he ollowing p ecompu ed in o ma ion on each allele p esen :
- Beacon
- Da ase
- Popula ion
- Gene ic Ances y G oup
- Genome Build
- Allele Coun
- Allele Numbe
- Homozygous Coun
- Hemizygous Coun
- Female Coun
- Male Coun
- A use - iendly cen al web applica ion o pe o m he que y
- Web applica ion should s a e “The in o ma ion on his websi e is no in ended o di ec
diagnos ic use o medical decision-making wi hou e iew by a gene ics p o essional.
Indi iduals should no change hei heal h beha iou solely on he basis o in o ma ion
con ained on his websi e. I you ha e ques ions abou he in o ma ion con ained on his
websi e, please see a heal hca e p o essional.” - om
h ps://clinicalgenome.o g/abou / o simila
Desc ip ion:
- Use isi s a web applica ion ha looks some hing like he ollowing:
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#:
usGdi02
S o y name:
Look up a ian summa y da a in and ac oss GDI da ase s
T igge ed by Use Role:
Resea che and/o heal h p o essional
Au ho s and Con ibu o s:
LW, GC, TP, CHF
- Demo exis s he e: h ps://a -b owse -demo.ega-a chi e.o g/
- The use pe o ms a genomic que y sea ching o a a ian using he o ma ch -pos-
e -al h ough GDI’s ede a ed que ying sys em, wi h he abili y o speci y he genome
build and coho /da ase (o all coho s/da ase s)
Pos condi ions:
- The ou pu should look some hing like:
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#:
usGdi02
S o y name:
Look up a ian summa y da a in and ac oss GDI da ase s
T igge ed by Use Role:
Resea che and/o heal h p o essional
Au ho s and Con ibu o s:
LW, GC, TP, CHF
- This ype o da a could be used o :
- Clinical and esea ch a ian in e p e a ion (o e seen by a gene ics
p o essional)
- Check i you pa ien ’s a ian is p esen in simila pa ien coho s (e.g.
h ps://epi25.b oadins i u e.o g/)
Needs discussion and cla i ica ion:
- One possible unc ion o GDI would be o c ea e a gnomAD-like po al bu o he
Eu opean popula ion and o disease coho s. Wi h GoE da a, his could be achie ed bu
i migh no be he goal o he p ojec . Mo eo e , he emaining da ase s and da a
collec ions wi hin GDI could be included in o his “ esou ce/se ice” bu o do so, he
da a access policy and i s g anula i y (beyond public/p i a e) needs o be de ined and
discussed.
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GWAS analysis
#:
usGdi05
S o y name:
GWAS analysis
T igge ed by Use Role:
Resea che
Au ho s and Con ibu o s:
F om D7.5 - In ec ious diseases use case
Use s o y desc ip ion:
A esea che needs o que y he GDI in as uc u e and pe o m a apid Genome-Wide
Associa ion S udy (GWAS) in o de o alida e isk a ian s de e mining he se e i y o COVID-
19. As GWAS equi es la ge sample sizes, mul iple compa able da ase s a e o en needed.
The goal is o ind human genomic da ase s ha include pa ien s wi h se e e COVID-19.
Pe o ming a GWAS in a ede a ed analysis scheme.
As a esea che , I wan o pe o m a GWAS ac oss mul iple compa able popula ion da ase s.
P econdi ions:
The esea che mus be au hen ica ed and au ho ised o GDI
Desc ip ion:
- The esea che logs in o he GDI pla o m (ujGdi01).
- The esea che needs o que y and il e he Cen al Da a Ca alogue (ujGdi02) o bo h
human genomic da a (i.e. SNPs, a ian s) and pheno ypic da a associa ed wi h COVID-
19 se e i y (i.e. hospi alisa ion, ICU admission, mo ali y).
- The GDI e u ns esul s, which could include human genomic da ase s anno a ed wi h
Co id-19 se e i y indica o s and po en ially o he pheno ypic in o ma ion, ound on one
o mul iple nodes o he ne wo k.
- The esea che applies o da a access o 1+MG da a (ujGdi04) and he Da a Access
Commi ee g an s he access (ujGdi05).
- The esea che accesses he anno a ed gene ic sequence da a o u he analysis. The
esea che execu es he analysis by dis ibu ing an in e ope able analysis pipeline
ac oss ede a ed loca ions (ujGdi08). The esea che can add a wo k low o he
secu e p ocessing en i onmen (SPE) (ujGdi10).
- The esea che can download he esul s om his esea ch esul s accoun o u he
p ocessing (ujGdi09).
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GWAS analyses ac oss ede a ed nodes
#:
usGdi05.1
S o y name:
GWAS analyses ac oss ede a ed nodes
T igge ed by Use Role:
Resea che
Au ho s and Con ibu o s:
F om D7.5 - 1+MG/B1MG use case
Use s o y desc ip ion:
As a esea che , I wan o pe o m a GWAS ac oss mul iple compa able popula ion da ase s.
This is an ex ension o usGdi05.
The goal is o iden i y genes associa ed wi h a pa icula disease o ai using p o ided whole
genomes. The p ima y ou pu o a GDI GWAS analysis is a lis o P alues, e ec sizes and hei
di ec ions gene a ed om he associa ion es s o all es ed gene ic a ian s wi h a pheno ype
o in e es .
P econdi ions:
- The esea che mus be au hen ica ed and au ho ised o GDI
- Rele an disease o ai and WGS da a mus be a ailable o coho building (ujGdi02)
Desc ip ion:
- The esea che logs in o he GDI pla o m (ujGdi01)
- The esea che needs o de ine he s udy coho using diseases o ai condi ions
(ujGdi03)
- The GDI e u ns esul s, which include he lis o human genomic da ase s ha ha e
speci ied disease o ai s.
- The esea che applies o da a access o 1+MG da a (ujGdi04) and he Da a Access
Commi ee g an s he access (ujGdi05).
- I a esea che ge s he app o al, hen he esea che can access gene ic sequence da a
indi ec ly by using p ede ined GWAS pipelines.
- The esea che execu es he GWAS analysis by dis ibu ing GWAS pipelines o ede a ed
p ocessing loca ions (ujGdi08 and ujGdi10). Indi idual pa icipan s' da a s ay wi hin
he coun y.
- The esea che ge s he ele an GWAS esul da a (like lis o P alues, Manha an plo s
e c) o his esea ch esul s accoun .
- The esea che can download he esul s om his esea ch esul s accoun o u he
p ocessing (ujGdi09).
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Recalib a ion o polygenic isk sco es
#:
usGdi06
S o y name:
Recalib a ion o polygenic isk sco es
T igge ed by Use Role:
Resea che
Au ho s and Con ibu o s:
F om D7.5 - Genome o Eu ope use case
Use s o y desc ip ion:
As a esea che , I wan o de elop PRSs so ha hey accu a ely p edic disease isk o
indi iduals in a speci ic ances y popula ion.
A esea che wan s o imp o e he accu acy o polygenic isk sco es (PRS) o p edic ing
disease isk in a speci ic ances y popula ion. The o iginal PRS was de eloped using da a om
ano he ances y g oup, bu he esea che needs o adjus he PRS o be e ec i e o
indi iduals o he speci ic ances y in hei s udy.
The goal is o ind human genomic da a om mul iple popula ions. This da a includes bo h
gene ic in o ma ion and heal h eco ds, such as he p esence o absence o he disease o
in e es . Subsequen ly, he PRS can be ecalcula ed in he iden i ied da ase .
P econdi ions:
The esea che mus be au hen ica ed and au ho ised o GDI
Desc ip ion:
- The esea che logs in o he GDI pla o m (ujGdi01).
- The esea che will cons uc a Beacon que y (ujGdi03), i.e. he esea che inpu s he
de ails o he a ian s used in he o iginal PRS in o GDI’s Beacon Ne wo k, asking
whe he he a ian is p esen in mul iple popula ion da ase s.
- The GDI e u ns esul s, which could include he lis o human genomic da ase s
oge he wi h a summa y on g oup le el, i.e. he equency o he a ian in he
popula ion. Only da ase s con aining a leas a p ede ined pe cen age (cu o ) o he
equi ed a ian s a e e ained.
- The esea che applies o da a access o 1+MG da a (ujGdi04) and he Da a Access
Commi ee g an s he access (ujGdi05).
- The esea che accesses gene ic sequence da a. The esea che execu es he analysis
(PRS) by dis ibu ing an in e ope able analysis pipeline ac oss ede a ed loca ions
(ujGdi08). The esea che can add a wo k low o he secu e p ocessing en i onmen
(SPE) (ujGdi10). Indi idual pa icipan s' da a s ay wi hin he coun y.
- The esea che can download he esul s om his esea ch esul s accoun o u he
p ocessing (ujGdi09).
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Ances y-speci ic impu a ion
#:
usGdi07
S o y name:
Ances y-speci ic impu a ion
T igge ed by Use Role:
Resea che
Au ho s and Con ibu o s:
F om D7.5 - Genome o Eu ope use case
Use s o y desc ip ion:
A esea che wan s o impu e a gene ic da ase using ances y-speci ic e e ence panels
The goal is o impu e missing gene ic da a using a mul i-e hnic e e ence panel (Genome o
Eu ope-GoE), which can cap u e ances y-speci ic gene ic a ian s mo e e ec i ely han
gene al panels. This equi es lea ning co ela ion pa e ns be ween SNPs in he GoE da a
( e e ence panel), hen using hese o in e (impu e) he missing geno ypes in a new sample.
Typically, ±1M a ian s a e measu ed, and hen impu ed owa ds >40M a ian s using he
co ela ion da a.
P econdi ions:
The esea che mus be au hen ica ed and au ho ised o GDI
Desc ip ion:
- The esea che logs in o he GDI pla o m (ujGdi01).
- The esea che needs o que y and il e he Cen al Da a Ca alogue (ujGdi02) ( il e
on ances y) o mul i-e hnic e e ence panels.
- The GDI e u ns esul s, which could include agg ega ed e e ence panels.
- The esea che applies o da a access o 1+MG da a (ujGdi04) and he Da a Access
Commi ee g an s he access (ujGdi05).
- The esea che accesses he e e ence panels (agg ega ed da a). The esea che
execu es he analysis (impu a ion o gene ic da ase s).
- The esea che can download he esul s om his esea ch esul s accoun o u he
p ocessing (ujGdi09).
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Annex
Au ho s and Con ibu o s
CHF: Ca les He nandez-Fe e
EB: Elisa Bene i
GB: Gab iele Bucci
EGJ: Eugenio González Jiménez
FG: F ancesca Geno a
GG: Gio gia Gandol i
GK: Giselle Ke y
JAMB: Je oen Belien
JMF: Jose Ma ia Fe nandez
JR: Jo di Rambla
LC: Laia Codó
LP: Lau a Po ell
LW: Lau a Whelan
MM: Ma co Mo elli
ND: Nicolás Díaz
SCG: Sal ado Capella-Gui ié ez
GC:
TP:
Documen a ion
- Da a eques low p oposal: Miles one 7 Coo dina ion - V1.1
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P oposed GDI Access Wo k low
Figu e 1: P oposed GDI / 1+MG Da a Access wo k low
