from sddb import Catalog
cohort = Catalog().collection("doi-10-1038-s41586-022-05023-2")
cohort.members # the 23 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="doi-10.1038/s41586-022-05023-2")
coll.ordered_artifacts.to_dataframe() # the 23 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection doi-10-1038-s41586-022-05023-2 --dest data/Licenses: 23 CC BY-NC-SA 4.0
Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer<sup>1</sup>. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics<sup>2</sup> to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.
@article{Erickson_2022,
title = {Spatially resolved clonal copy number alterations in benign and malignant tissue},
volume = {608},
ISSN = {1476-4687},
url = {http://dx.doi.org/10.1038/s41586-022-05023-2},
DOI = {10.1038/s41586-022-05023-2},
number = {7922},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
author = {Erickson, Andrew and He, Mengxiao and Berglund, Emelie and Marklund, Maja and Mirzazadeh, Reza and Schultz, Niklas and Kvastad, Linda and Andersson, Alma and Bergenstråhle, Ludvig and Bergenstråhle, Joseph and Larsson, Ludvig and Alonso Galicia, Leire and Shamikh, Alia and Basmaci, Elisa and Díaz De Ståhl, Teresita and Rajakumar, Timothy and Doultsinos, Dimitrios and Thrane, Kim and Ji, Andrew L. and Khavari, Paul A. and Tarish, Firaz and Tanoglidi, Anna and Maaskola, Jonas and Colling, Richard and Mirtti, Tuomas and Hamdy, Freddie C. and Woodcock, Dan J. and Helleday, Thomas and Mills, Ian G. and Lamb, Alastair D. and Lundeberg, Joakim},
year = {2022},
month = Aug,
pages = {360–367}
}