notch2 backstage
DESCRIPTION
Description of the bioinformatics side of our paper "Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis". published in Nature Genetics. http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.778.html. doi:10.1038/ng.778.TRANSCRIPT
NOTCH2Backstage
http://www.flickr.com/photos/constuv/4319650519
Pierre Lindenbaum PhDUMR915 – Institut du thorax
Nantes, Francehttp://plindenbaum.blogspot.com
... the story begins inNantes / France ,
in november 2010...
here
... in the “Institut du Thorax”(INSERM/UMR915)
...we're workingon ...
Hajdu–Cheney syndrome
Dr. Cedric LeCaignec
Hajdu-Cheney syndromeis a rare skeletal disorder
characterized bythe association of facial anomalies,
radiological findings &premature loss of permanent teeth
http://commons.wikimedia.org/wiki/File:Autodominant.jpg
Although most cases are sporadic, few familial transmissions suggest autosomal dominant inheritance
We have sequenced
the exomes of 6 unrelated patients with
Hajdu-Cheney syndrome.
http://en.wikipedia.org/wiki/File:Exome_Sequencing_Workflow_1a.png
http://en.wikipedia.org/wiki/Exome_sequencing
Exome Sequencing
We'll soon receiveour
“Exome Sequencing”data from
Integragen .
Can you help usto analyze the
data ?
By chance,I worked as a
Bioinformaticianat Integragen
(Evry, France) for 7 years !
I know them all ! :-)
People fromIntegragen
in myLinkedIn Network
INTEGRAGEN
http://www.flickr.com/photos/sweetlog/1108966791
it made the conversations easier when we called Integragen to get some insights about the data....
Allo Pierre ? Comment vas-tu yau'd'poil ?
We received a DVD containing the genotypes...
... and a hard-drive containing the raw data.
... the data for each sample look like this...
#CHROM POS REF ALTchr4 58703510 A Gchr19 4068794 C Tchr15 93625392 A Gchr1 73570071 A Cchr16 62799884 A Gchr19 2234072 GG Gchr19 3316536 gg gchr19 3158826 g gGchr13 22464550 g gAchr8 80435887 C Tchr4 130829885 A Gchr12 85102835 C Tchr8 56140941 A Gchr2 179036301 A Tchr16 34927854 C Tchr10 104324871 G Achr4 81581119 T C
LinuxJDK6
Eclipse
Coffee
The first program I wrote was a command-line tool...
http://code.google.com/p/code915/source/browse/trunk/tools/src/java/fr/inserm/umr915/tools/Integragen20101022.java
..basically, the program is a set of filters to select the interesting mutations.
http://code.google.com/p/code915/source/browse/trunk/tools/src/java/fr/inserm/umr915/tools/Integragen20101022.java
Google-code was used as a repository for the source-code.
… and the program generated a wiki code that we put on our internal wiki...
Can you test with a minimal DEPTH=20 ?
And with minimal number of affected
samples per SNP = 2 ?
And with minimal number of affected
samples per gene = 4 ?Can you remove
all the known SNPs ?
Did we try fix the maximum
number of SNPs per gene ?
Did we ever find this gene ?
Did you include the results from
Polyphen ?
What time is it ?
http://www.flickr.com/photos/ohm17/162622755
People want to get their hands dirty
http://www.jensroesner.de/wgetgui/#screen
A Graphical User
Interface (GUI)
was needed...
A quick access to the data was required
http://www.oracle.com/technetwork/database/berkeleydb/overview/index-093405.html
The key/value model
Example: filtering on Polyphen2
filters...
Variations have been filtered.What are the remaining transcripts ?
… too many transcripts ?
… winnner !
The software is alwaysup-to-date
WebStart was used to deploy the application
I want to use your program from my home
this week-end....
Proxy+
WEBSTART
I created an executable JAR and the program was distributed via
http://www.dropbox.com
http://www.flickr.com/photos/hurty/401880903/
Filter...
Filter...
Filter...
LOSER
LOSER...
Filter...
Filter...
Filter...
http://commons.wikimedia.org/wiki/File:Hourglass.jpg
Meanwhile, we suspected that another team was working on the very same topic ...
We found 78 genes, which were affected by
distinct missense variants in three
unrelated patients
In contrast, only 5 genes
ARSD, NOMO3, NOTCH2,
OR2T35, PCTK3
were inactivated by nonsense mutations in
two unrelated patients
http://www.ncbi.nlm.nih.gov/gene/4853
“NOTCH2 appeared to be an outstanding functional
candidate”
By checking unfiltered
sequencing data for any missed genetic
variant within NOTCH2
we identified an additional
nonsense mutationin a third patient.
Next, we searched for frameshift mutations in NOTCH2 and
identified small indels in two
additional patients.
http://commons.wikimedia.org/wiki/File:Linen_tester.jpg
?In the remaining patient, no NOTCH2 mutation could be identified
Sanger sequencing confirmed the heterozygous
NOTCH2mutations
http://commons.wikimedia.org/wiki/File:Sanger_sequencing_read_display.gif
We tested inheritance in two families:both mutations occurred de novo.
+/m
+/+
+/+
http://commons.wikimedia.org/wiki/File:OldFamily.JPG
November 5th 2010 : NOTCH2
Where are the mutations in NOTCH2 ?....
Are they located
before or after the “PEST” domain ?
http://plindenbaum.blogspot.com/2010/11/blastxmlannotations.html
EGF repeats (n=36) TMDANK
NLSPEST
LNR
NLSRAM
NOTCH2
mutation mutation
mutation
mutation
mutation
Again, our internal wiki was used to store the informations
about NOTCH2
Subject: Notification about reviewers of NG-xxxxxxx Le Caignec from Nature GeneticsDe: [email protected]: Mar 30 novembre 2010 19:49To: Cedric Lecaignec--------------------------------------------------------------------------
Dear Dr. Le Caignec,Thank you for submitting your paper, NG-xxxxx Le Caignec, to NatureGenetics. I'm writing to let you know that we have decided to send yourmanuscript for peer review. We usually ask our referees to respond withintwo to three weeks, and we will make every attempt to encourage them tomeet this deadline. Once we have received the reviews and made a decisionabout your paper, we will contact you by email.
Sincerely,XXSenior EditorNature Genetics
10th December 2010
Dear Dr. Le Caignec,Your manuscript "Truncating mutations in the last exon of NOTCH2 cause arare skeletal disease with osteoporosis" has now been seen by tworeferees, and you will see from the accompanying comments that, whereasthey find your work interesting (as do we), they have raised points thatmust be addressed through appropriate revisions and to their satisfaction before we can proceed further.
Date: Ven 4 février 2011 19:23To: Cedric LecaignecIn reply please quote: NGxxxxx Le Caignec
I am delighted to say that your manuscript "Truncating mutations in thelast exon of NOTCH2 cause a rare skeletal disorder with osteoporosis" hasbeen accepted for publication in an upcoming issue of Nature Genetics.
… just on time !
Our challengers
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.778.html
2011-03-07.our paper was
available on“Nature Genetics”
....
… side-by-sideto our
challengers ....
http://twitter.com/#!/yokofakun/status/44767830905856000
http://biostar.stackexchange.com/questions/6215/we-found-a-gene-involved-in-a-genetic-disease-now-what-is-the-todo-list
What's next ?
What's next ? Wikipedia
What's next ? Gene RIF
http://www.wikigenes.org/e/gene/e/4853.html
What's next ? WikiGenes.
Dear Colleague,I have forwarded your message to the OMIM editors for their consideration.Note that the editors of OMIM attempt to include the essential references f=or a particular topic, not necessarily everything that has been published. = In addition, a neighboring feature has been applied to OMIM that links add=itional, relevant articles from MEDLINE to each entry, thereby ensuring tha=t all relevant articles are easily retrievable.The OMIM editors will contact you directly should they require any further =information.Best regards,
NCBI User Services-----Original Message-----From: Pierre LindenbaumTo: NLM/NCBI InfoSubject: OMIM
Hi OMIM,here are two suggestions for OMIM ID. 102500
http://www.ncbi.nlm.nih.gov/pubmed/21378989
Nat Genet. 2011 Mar 6."Truncating mutations in the last exon of NOTCH2 cause a rare skeletal=20disorder with osteoporosis."Isidor B, Lindenbaum P, Pichon O, B=E9zieau S, Dina C, Jacquemont S,=20Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A,=20Faivre L, Cormier-Daire V, Redon R, Le Caignec C.
http://www.ncbi.nlm.nih.gov/pubmed/21378985
Nat Genet. 2011 Mar 6"Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe=20and progressive bone loss."Simpson MA, Irving MD, Asilmaz E, Gray MJ, Dafou D, Elmslie FV, Mansour=20S, Holder SE, Brain CE, Burton BK, Kim KH, Pauli RM, Aftimos S, Stewart=20H, Kim CA, Holder-Espinasse M, Robertson SP, Drake WM, Trembath RC.
What's next ?
What's next ? : Uniprot
http://www.flickr.com/photos/constuv/4319650519
Nantes:
Bertrand Isidor Olivier Pichon,Stéphane Bézieau,Christian Dina,Sébastien Jacquemont,Dominique Martin-Coignard,Christel Thauvin-Robinet,Martine Le MerrerJean-Louis MandelAlbert DavidLaurence FaivreValérie Cormier-DaireRichard RedonHadja EldjouziCédric Le Caignec
Integragen (Evry):
Melanie LetexierBerengere GeninJean-Paul SaraivaCharles MarcaillouFrancis RousseauEmmanuel Martin
ThankYou
http://www.flickr.com/photos/constuv/4319650519