Cloud computing for genomic data analysis and collaboration

B Langmead, A Nellore - Nature Reviews Genetics, 2018 - nature.com
Next-generation sequencing has made major strides in the past decade. Studies based on
large sequencing data sets are growing in number, and public archives for raw sequencing …

Data lakes, clouds, and commons: a review of platforms for analyzing and sharing genomic data

RL Grossman - Trends in Genetics, 2019 - cell.com
Data commons collate data with cloud computing infrastructure and commonly used
software services, tools, and applications to create biomedical resources for the large-scale …

The repertoire of mutational signatures in human cancer

LB Alexandrov, J Kim, NJ Haradhvala, MN Huang… - BioRxiv, 2018 - biorxiv.org
Somatic mutations in cancer genomes are caused by multiple mutational processes each of
which generates a characteristic mutational signature. Using 84,729,690 somatic mutations …

[HTML][HTML] Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations

M Fujita, R Yamaguchi, T Hasegawa, S Shimada… - …, 2020 - thelancet.com
Background The tumor microenvironment can be classified into immunologically active"
inflamed" tumors and inactive" non-inflamed" tumors based on the infiltration of cytotoxic …

[HTML][HTML] Global impact of somatic structural variation on the DNA methylome of human cancers

Y Zhang, L Yang, M Kucherlapati, A Hadjipanayis… - Genome biology, 2019 - Springer
Background Genomic rearrangements exert a heavy influence on the molecular landscape
of cancer. New analytical approaches integrating somatic structural variants (SSVs) with …

[HTML][HTML] XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature

AA Yurchenko, I Padioleau, BT Matkarimov… - Nature …, 2020 - nature.com
Recent studies demonstrated a dramatically increased risk of leukemia in patients with a
rare genetic disorder, Xeroderma Pigmentosum group C (XP-C), characterized by …

Aberrant PRDM9 expression impacts the pan-cancer genomic landscape

AA Houle, H Gibling, FC Lamaze… - Genome …, 2018 - genome.cshlp.org
The binding of PRDM9 to chromatin is a key step in the induction of DNA double-strand
breaks associated with meiotic recombination hotspots; it is normally expressed solely in …

Making use of cancer genomic databases

CJ Creighton - Current protocols in molecular biology, 2018 - Wiley Online Library
The vast amounts of genomic data now deposited in public repositories represent rich
resources for cancer researchers. Large‐scale genomics initiatives such as The Cancer …

Progress toward cancer data ecosystems

RL Grossman - The Cancer Journal, 2018 - journals.lww.com
One of the recommendations of the Cancer Moonshot Blue Ribbon Panel report from 2016
was the creation of a national cancer data ecosystem. We review some of the approaches …

[HTML][HTML] sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

A Kuzniar, J Maassen, S Verhoeven, L Santuari… - PeerJ, 2020 - peerj.com
Structural variants (SVs) are an important class of genetic variation implicated in a wide
array of genetic diseases including cancer. Despite the advances in whole genome …