Question: Where To Find The Sequence Data About Leukemia?
1
gravatar for jlshi.nudt
6.1 years ago by
jlshi.nudt180
China
jlshi.nudt180 wrote:

I want to find sequence data about leukemia patients as much as possible. but I only find a few records in SRA database of NCBI, and find little information about the sample , e.g. the karytype, age et.al. Where to find more such database? thank you.

sequence • 1.9k views
ADD COMMENTlink modified 6.1 years ago by Chris Miller20k • written 6.1 years ago by jlshi.nudt180

Broad has some data, and some more

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Pavel Senin1.9k
2
gravatar for Medhat
6.1 years ago by
Medhat8.3k
Texas
Medhat8.3k wrote:

Whole genome sequencing of core-binding factor leukemia

Leukemia, Myeloid, Acute

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Medhat8.3k

Thank you. That's very helpful. I want to find as many as possible.

ADD REPLYlink written 6.1 years ago by jlshi.nudt180

what do you want to find more?

ADD REPLYlink written 6.1 years ago by Medhat8.3k
1
gravatar for Raghul
6.1 years ago by
Raghul200
Italy
Raghul200 wrote:

Hi I remember some 10 years ago my genetics teacher told me McKusick built a catalog of human genes and phenotypes called OMIM (Online Mendelian Inheritance in Man ) & I checked now in NCBI there is even one for animals (OMIA). Please go to NCBI website & select OMIM, type leukemia, hope u get what u want

good luck raghul

ADD COMMENTlink written 6.1 years ago by Raghul200
1

Online Mendelian Inheritance in Man (OMIM) can now be found at: http://omim.org/

ADD REPLYlink written 6.1 years ago by Hamish3.1k
1
gravatar for Chris Miller
6.1 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

The TCGA consortium just published a study of 200 sequenced AML patients that were really comprehensively characterized (50 wgs, 150 exomes, + rnaseq + microarrays + methylation arrays, etc). Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

The data for this project is available through the TCGA Data Portal and CGHub.

(full disclosure - I was heavily involved in this project)

ADD COMMENTlink written 6.1 years ago by Chris Miller20k

I just discovered this paper via a Nature Reviews Clinical Oncology Research Highlight (http://www.nature.com/nrclinonc/journal/v10/n6/full/nrclinonc.2013.81.html). Huge effort and great work! This is a rich source of sequencing data for AML.

ADD REPLYlink written 6.1 years ago by Sebastian Boegel460
0
gravatar for Hamish
6.1 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

Well a quick and dirty search using the EBI Search gives some stuff you might want to look through:

http://www.ebi.ac.uk/ebisearch/search.ebi?query=leukemia+homo+sapiens&db=allebi

As does a search in GWAS Central:

https://www.gwascentral.org/search?q=leukemia

The following sites may also be useful:

Note: due to the restrictions on the publication of patent data, some of the information you are after may be hard to find, or require you or your institute to sign a confidentiality agreement.

ADD COMMENTlink written 6.1 years ago by Hamish3.1k

Thank you. That's the best collection so far.

ADD REPLYlink written 6.1 years ago by jlshi.nudt180
0
gravatar for Sebastian Boegel
6.1 years ago by
Germany
Sebastian Boegel460 wrote:

Another consortium (comparable to TCGA) is ICGC. I had a quick look and the also have CLL studies. As for TCGA, you (your group) needs to apply to have access to this data. Here is an overview of the datasets, they have: https://www.ebi.ac.uk/ega/dacs/EGAC00001000010.

BTW: this is only NGS data (RNA-Seq, whole genome, whole exome).

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Sebastian Boegel460

FWIW the earlier query in EBI Search (http://www.ebi.ac.uk/ebisearch/search.ebi?query=leukemia+homo+sapiens&db=allebi) includes the data from "The European Genome-phenome Archive (EGA)", as well as data from more traditional sequence and expression databases.

ADD REPLYlink written 6.1 years ago by Hamish3.1k
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