2014-04-30: More than 2500 publications registered in Progenetix

The Progenetix database now lists 2501 publications in which whole genome copy number screening experiments in cancer samples were reported. These include comparative genomic hybridisation experiments, genomic array data sets as well as increasingly reports of whole genome or exome (WGS/WES) screening studies.

last edit 2014-04-30
[display] [permalink] [edit] [top]

2014-04-11: Large lung cancer study added

We've just integrated 1033 copy number profiles from the The Clinical Lung Cancer Genome Project (CLCGP) and Network Genomic Medicine (NGM) study. It is a very nice and comprehensive dataset, including clinical followup etc. Make sure to read the article!

last edit 2014-04-11
[display] [permalink] [edit] [top]

2014-03-14: Array-based analyses in the current technological landscape

We have started a new blog, with an article discussing some aspects of array based molecular analyses and their utility in the current technological landscape. Enjoy! Comments are welcome...

last edit 2014-03-20
[display] [permalink] [edit] [top]

2014-02-18: New Progenetix server hardware

We just switched to some new server hardware - small & black ... Fingers crossed - please let us know about oddities.

last edit 2014-02-18
[display] [permalink] [edit] [top]

2014-02-03: Our arrayMap based "Chromothripsis-like patterns" article is out

With PMID 24476156, PubMed now lists our discussion of clustered genomic copy numbers imbalances in cancer, which correspond to copy number aberration patterns commonly referred to as "Chromothripsis".

Based on the analysis of ~20'000 genomic array datasets from our arrayMap database, we discuss features associated with these patterns and suggest that they represent a number of, frequently cancer type related, genomic aberration types, beyond a well defined single "Chromothripsis" phenomenon.

The PDF of the article can be downloaded directly from here .... Open Access, naturally - Enjoy!

last edit 2014-02-04
[display] [permalink] [edit] [top]

2013-12-13: Progenetix now collects cancer genome / exome sequencing publications

We have started to list WES / WGS publications of cancer genomes in the Progenetix literature collection. For now, we just try to extract copy number aberration data if it is annotated in a compatible format.

The first example here is the publication by Bea et al. of whole exome sequencing data in mantle cell lymphomas. This publication is exemplary in providing supplementary information, including listing of CNA regions from the WES data, and deposition of corresponding SNP (will be added to arrayMap later) and expression arrays in GEO.

last edit 2013-12-13
[display] [permalink] [edit] [top]

2013-11-13: New publication - "Progenetix: 12 years of oncogenomic data curation"

Our new database update publication

  • "Progenetix: 12 years of oncogenomic data curation"

which had been deposited at http://arxiv.org/abs/1311.2757 has now been published at Nucleic Acids Research, as part of NAR's 2014 database issue:

Open Access ...

Enjoy!

last edit 2013-11-13
[display] [permalink] [edit] [top]

2013-11-11: Improved search options, now with autocomplete

We have added autocomplete options to sample and publication search, and integrated a search across multiple fields (authors, title, abstract, PMID) for the publication search.

Enjoy!

last edit 2013-11-11
[display] [permalink] [edit] [top]

2013-11-08: Maps!

We have implemented a map display for the currently selected articles or samples.

Essentially, all samples of the current subset / search result are projected to their origin, determined from the main institution associated with the publication.

This feature should come in particularly handy when e.g. finding out which institutions are especially active in a given area of cancer genome research. However, for the sample driven listings, this depends on the availability of the sample data through Progenetix/arrayMap.

Enjoy!

last edit 2013-11-08
[display] [permalink] [edit] [top]

2013-10-30: SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome.

Michael has been co-author of another non-cancer genetics publication:

Krieger, M., A. Roos, C. Stendel, K. G. Claeys, F. M. Sonmez, M. Baudis, P. Bauer, A. Bornemann, C. de Goede, A. Dufke, R. S. Finkel, H. H. Goebel, M. Haussler, H. Kingston, J. Kirschner, L. Medne, P. Muschke, F. Rivier, S. Rudnik-Schoneborn, S. Spengler, F. Inzana, F. Stanzial, F. Benedicenti, M. Synofzik, A. Lia Taratuto, L. Pirra, S. K. Tay, H. Topaloglu, G. Uyanik, D. Wand, D. Williams, K. Zerres, J. Weis, and J. Senderek. SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome. Brain (2013) PubMed

last edit 2013-11-11
[display] [permalink] [edit] [top]

2013-09-26: New option for filtering focal copy number aberrations

When looking for focal copy number aberrations, so far min/max values could be used to limit CNAs to a given size range. A typical scenario would be to e.g. set the "max" to "5000" when querying a given gene, thereby limiting the size of the called segment involving the gene to 5Mb - this is pretty much a focal hit (though it still may involve quite a number of other potential targets).

However, this method is not very specific: e.g. a whole chromosome loss in a "medium quality" array may present as hundreds of small segments, thereby triggering "focal" calls.

The addition or sole use of the new "MAX COVERAGE" option adds another layer of "selactability". A value of 5000 there means that only gene hits are evaluated, if in the interval "gene CDR start - 5000" to "gene CDR end + 5000" all segments of the requested type (gain/1 or loss/-1) do not exceed 5000 kb. (A true sliding window approach around the target may be theoretically superior, but in practice would not make a lot of difference.

As always, comments appreciated ...

last edit 2013-11-08
[display] [permalink] [edit] [top]

2013-07-11: Haoyang Cai - a new arrayMap PhD from the Baudis group

Congratulations to Haoyang, who successfully defended his thesis on July 11, 2013. A substantial part of his project was the assembly of the arrayMap resource, which we reported in a 2012 (PLoS ONE paper)[http://www.ncbi.nlm.nih.gov/pubmed/22629346].

And thanks to the other members of his thesis committee - Christian von Mering, Mark Robinson, Homayoun Bagheri and Nuria Lopez-Bigas!

last edit 2013-11-08
[display] [permalink] [edit] [top]

2013-07-10: Thesis Defence Haoyang Cai: Characterization of Cancer Genomes through Systematic Analyses of Oncogenomic Data Assemblies

Haoyang Cai from the Baudis group will present the results of his PhD thesis on Thursday, July 11 in Y55 L08, Irchel Campus. Guests are welcome; the presentation starts at 15:00.

haoyang_cai_phd_thesis_defense.pdf [PDF]

last edit 2013-11-08
[display] [permalink] [edit] [top]

CNZ Zurich Joint Cancer meeting: Michael Baudis - Genomic copy number aberrations in cancer - Patterns, Targets, Resources

As part of the joint cancer meeting of the Cancer Network Zurich, Michael Baudis will present his group's Progenetix and arrayMap resources and some associated research projects.

Other speakers:

  • Martin Baumgartner: Imaging and molecular characterization of cancer cell motility
  • Maurizio Provenzano: Diagnostic/prognostic procedures and treatment options for prostate cancer

Room: USZ PATH C22

Time: 16:30H - 18:00H

last edit 2013-06-17
[display] [permalink] [edit] [top]

First copy number profiling data from methylation arrays added

We have added the first series of copy number aberration data from methylation arrays (Sturm et al., PMID 23079654) to Progenetix and arrayMap. Among overall 210 glioma saples, the dataset contains 69 paediatric/young adult DIPG/high grade gliomas which are included in the (DIPG project)[http://dipg.progenetix.org].

We will use this as a pilot project, to work on a future general use of this type of molecular screening data. However, we deem it worthwhile to provide the data in its current state - and we are very excited about these developments.

last edit 2013-04-27
[display] [permalink] [edit] [top]

Haoyang Cai presenting chromothripsis data at Cancer Network Zurich retreat

Haoyang will present his results from the analysis of chromothripsis-like genome patterns at this year's CNZ retreat in Grindelwald:

  • Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genomes
last edit 2013-04-11
[display] [permalink] [edit] [top]

Spring collaboration meeting in Timisoara

From 2013-03-21 - 2013-03-23, the Swiss-Romanian cutaneous NHL collaboration meets in Timisoara.

last edit 2013-03-26
[display] [permalink] [edit] [top]

30449 cancer genome profiles from 1001 publications now included in Progenetix

By adding some new data sets and annotating some more of the evaluated data from arrayMap, Progenetix now has more than 30000 cancer genome copy number profiles, from 1001 publications. The data consists of 20531 chromosomal CGH and 10024 genomic array profiles, and covers 364 diagnostic entities according to ICD-O 3.

last edit 2013-03-01
[display] [permalink] [edit] [top]

Progenetix and arrayMap API for cancer genome copy number aberration frequency profiles

last edit 2013-02-07
[display] [permalink] [edit] [top]

BIO612: Haoyang Cai: Focal Copy Number Changes in Cancer and Genome Structure

last edit 2013-01-16
[display] [permalink] [edit] [top]

www.compbio.ch - The new web address for @compbiozurich

last edit 2013-01-11
[display] [permalink] [edit] [top]

DIPG data collaboration meeting in Zurich

last edit 2013-04-05
[display] [permalink] [edit] [top]

Happy New Year

last edit 2012-12-30
[display] [permalink] [edit] [top]

Progenetix and arrayMap status update

last edit 2012-12-28
[display] [permalink] [edit] [top]

Progenetix and arrayMap cancer genome database server errors

last edit 2012-12-27
[display] [permalink] [edit] [top]

CNA sample profile similarity search

last edit 2012-10-25
[display] [permalink] [edit] [top]

SEER categories in Progenetix and arrayMap

last edit 2012-10-22
[display] [permalink] [edit] [top]

arrayMap featured at the Journal of the National Cancer Institute

last edit 2012-08-29
[display] [permalink] [edit] [top]

New Progenetix article published at PLoS ONE

last edit 2012-08-27
[display] [permalink] [edit] [top]

Renal cell carcinoma paper published at BMC Cancer

last edit 2012-07-27
[display] [permalink] [edit] [top]

Nitin Kumar - a new @progenetix PhD

last edit 2012-07-10
[display] [permalink] [edit] [top]

Interface enhancements

last edit 2012-07-03
[display] [permalink] [edit] [top]

DIPG genomics data repository now hosted at dipg.progenetix.org

last edit 2012-06-24
[display] [permalink] [edit] [top]

CNA size filtering

last edit 2012-06-13
[display] [permalink] [edit] [top]

New interval options

last edit 2012-06-05
[display] [permalink] [edit] [top]

@progenetix | arrayMap Changes (- 2013-05-22)

last edit 2013-09-23
[display] [permalink] [edit] [top]

arrayMap and Progenetix interface update

last edit 2012-05-06
[display] [permalink] [edit] [top]

arrayMap manuscript accepted at PLoS ONE

last edit 2012-04-17
[display] [permalink] [edit] [top]

Progenetix & arrayMap RSS feed

last edit 2013-01-23
[display] [permalink] [edit] [top]

Search Samples

last edit 2012-03-26
[display] [permalink] [edit] [top]

Registration

last edit 2012-03-23
[display] [permalink] [edit] [top]

Search Posts