Where To Find The Sequence Data About Leukemia?

Question

[jlshi.nudt]

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.

[Pavel Senin]

Broad has some data, and some more

Answer 1

[Medhat]

Whole genome sequencing of core-binding factor leukemia

Leukemia, Myeloid, Acute

[jlshi.nudt]

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

[Medhat]

what do you want to find more?

Answer 2

[Raghul]

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

[Hamish]

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

Answer 3

[Chris Miller]

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)

[Sebastian Boegel]

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.

Answer 4

[Hamish]

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:

• Cancer Genome Atlas
• The Cancer Genome Project
• cBioPortal for Cancer Genomics

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.

[jlshi.nudt]

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

Answer 5

[Sebastian Boegel]

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).

[Hamish]

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.