Impact of somatic mutations and transcriptomic alterations on cancer aneuploidy

CENP-A overexpression promotes aneuploidy with karyotypic heterogeneity

(2021) Roshan L. Shrestha et al.   JOURNAL OF CELL BIOLOGY

Acquisition of aneuploidy drives mutant p53-associated gain-of-function phenotypes

(2021) Lindsay N. Redman-Rivera et al.   Nature Communications

Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies

(2021) Sushant Patkar et al.   Genome Medicine

Single-Chromosomal Gains Can Function as Metastasis Suppressors and Promoters in Colon Cancer

(2020) Anand Vasudevan et al.   DEVELOPMENTAL CELL

Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability

(2020) Noam Auslander et al.   Nature Communications

Characterization of tumors with ultralow tumor mutational burden in Japanese cancer patients

(2020) Keiichi Hatakeyama et al.   CANCER SCIENCE

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

(2020) Simone Zaccaria et al.   Nature Communications

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions

(2019) Vitor H. Teixeira et al.   NATURE MEDICINE

Mutational burden and signatures in 4,000 Japanese cancers provide insights into tumorigenesis and response to therapy

(2019) Keiichi Hatakeyama et al.   CANCER SCIENCE

Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas

(2019) Lawrence A. Donehower et al.   Cell Reports

Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients

(2019) Takeshi Nagashima et al.   CANCER SCIENCE

Tumor mutational burden analysis of 2,000 Japanese cancer genomes using whole exome and targeted gene panel sequencing

(2018) Keiichi HATAKEYAMA et al.   BIOMEDICAL RESEARCH-TOKYO

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas

(2018) David S. Guttery et al.   Oncotarget

Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death

(2018) Haley Hieronymus et al.   eLife

Mutant p53 as a guardian of the cancer cell

(2018) Fiamma Mantovani et al.   CELL DEATH AND DIFFERENTIATION

T-Cell–Inflamed Gene-Expression Profile, Programmed Death Ligand 1 Expression, and Tumor Mutational Burden Predict Efficacy in Patients Treated With Pembrolizumab Across 20 Cancers: KEYNOTE-028

(2018) Patrick A. Ott et al.   JOURNAL OF CLINICAL ONCOLOGY

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

(2018) Razvan Cristescu et al.   SCIENCE

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data

(2017) Hyung-Yong Kim et al.   Oncotarget

Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors

(2017) Keiichi Ohshima et al.   Scientific Reports

Next generation sequencing approach for detecting 491 fusion genes from human cancer

(2016) Kenichi URAKAMI et al.   BIOMEDICAL RESEARCH-TOKYO

Integrated next-generation sequencing analysis of whole exome and 409 cancer-related genes

(2016) Yuji SHIMODA et al.   BIOMEDICAL RESEARCH-TOKYO

Optimizing an ion semiconductor sequencing data analysis method to identify somatic mutations in the genomes of cancer cells in clinical tissue samples

(2016) Takeshi NAGASHIMA et al.   BIOMEDICAL RESEARCH-TOKYO

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

The presence of extra chromosomes leads to genomic instability

(2016) Verena Passerini et al.   Nature Communications

TP53Mutations in Hypodiploid Acute Lymphoblastic Leukemia

(2016) Evan Q. Comeaux et al.   Cold Spring Harbor Perspectives in Medicine

Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes

(2015) Razvan Cristescu et al.   NATURE MEDICINE

SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data

(2015) Zhongyang Zhang et al.   PLoS Computational Biology

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

(2014) Qiaonan Duan et al.   NUCLEIC ACIDS RESEARCH

EMT is the dominant program in human colon cancer

(2013) Andre Loboda et al.   BMC Medical Genomics

Aneuploidy, oncogene amplification and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells

(2013) H. M. Padilla-Nash et al.   CARCINOGENESIS

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

The PI3K–Akt mediates oncogenic Met-induced centrosome amplification and chromosome instability

(2010) Hyun-Ja Nam et al.   CARCINOGENESIS

Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis

(2009) Andrew J. Holland et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY