Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer

Somatic structural variant formation is guided by and influences genome architecture

(2022) Nikos Sidiropoulos et al.   GENOME RESEARCH

Cancer Statistics, 2021

(2021) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data

(2021) Miao Yu et al.   NATURE METHODS

Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

(2021) Xiaotao Wang et al.   NATURE METHODS

The pancreatic cancer genome revisited

(2021) Akimasa Hayashi et al.   Nature Reviews Gastroenterology & Hepatology

Principles of 3D compartmentalization of the human genome

(2021) Michael H. Nichols et al.   Cell Reports

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

(2021) Zhikun Wu et al.   Nature Communications

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

(2020) Isidro Cortés-Ciriano et al.   NATURE GENETICS

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

Pattern of invasion in human pancreatic cancer organoids is associated with loss of SMAD4 and clinical outcome

(2020) Wenjie Huang et al.   CANCER RESEARCH

Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia

(2020) Andreas Kloetgen et al.   NATURE GENETICS

LncRNA MIR31HG functions as a ceRNA to regulate c-Met function by sponging miR-34a in esophageal squamous cell carcinoma

(2020) Jie Chu et al.   BIOMEDICINE & PHARMACOTHERAPY

Pancreatic cancer

(2020) Jonathan D Mizrahi et al.   LANCET

Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

(2020) Leina Lu et al.   MOLECULAR CELL

Long-read sequencing for non-small-cell lung cancer genomes

(2020) Yoshitaka Sakamoto et al.   GENOME RESEARCH

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

(2020) Sergey Aganezov et al.   GENOME RESEARCH

Chromothripsis drives the evolution of gene amplification in cancer

(2020) Ofer Shoshani et al.   NATURE

Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

(2019) Luis Augusto Eijy Nagai et al.   BMC Medical Genomics

The aberrant expression or disruption of desmocollin2 in human diseases

(2019) Chao Sun et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

(2019) Minjun Yang et al.   Nature Communications

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

(2018) Maria Nattestad et al.   GENOME RESEARCH

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Integrative detection and analysis of structural variation in cancer genomes

(2018) Jesse R. Dixon et al.   NATURE GENETICS

HiCDB: a sensitive and robust method for detecting contact domain boundaries

(2018) Fengling Chen et al.   NUCLEIC ACIDS RESEARCH

LncRNA MIR31HG targets HIF1A and P21 to facilitate head and neck cancer cell proliferation and tumorigenesis by promoting cell-cycle progression

(2018) Ru Wang et al.   Molecular Cancer

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network

(2018) Feda H. Hamdan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of desmoglein 2 promotes tumorigenic behavior in pancreatic cancer cells

(2017) Katharina Hütz et al.   MOLECULAR CARCINOGENESIS

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

(2017) Pengze Wu et al.   Nature Communications

Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis

(2016) Zehra Ordulu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

(2016) Faiyaz Notta et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Disordered methionine metabolism in MTAP/CDKN2A-deleted cancers leads to dependence on PRMT5

(2016) Konstantinos J. Mavrakis et al.   SCIENCE

Sequencing Structural Variants in Cancer for Precision Therapeutics

(2016) Geoff Macintyre et al.   TRENDS IN GENETICS

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Structural variation mutagenesis of the human genome: Impact on disease and evolution

(2015) James R. Lupski   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

Long noncoding RNA MIR31HG exhibits oncogenic property in pancreatic ductal adenocarcinoma and is negatively regulated by miR-193b

(2015) H Yang et al.   ONCOGENE

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Projecting Cancer Incidence and Deaths to 2030: The Unexpected Burden of Thyroid, Liver, and Pancreas Cancers in the United States

(2014) L. Rahib et al.   CANCER RESEARCH

Indexing Graphs for Path Queries with Applications in Genome Research

(2014) Jouni Siren et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Finding the active genes in deep RNA-seq gene expression studies

(2013) Traver Hart et al.   BMC GENOMICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

Diagnostic interpretation of array data using public databases and internet sources

(2012) Nicole de Leeuw et al.   HUMAN MUTATION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Reduced expression of desmocollin 2 is an independent prognostic biomarker for shorter patients survival in pancreatic ductal adenocarcinoma

(2011) Z. Hamidov et al.   JOURNAL OF CLINICAL PATHOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A copy number variation morbidity map of developmental delay

(2011) Gregory M Cooper et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Pancreatic Cancer

(2008) Anirban Maitra et al.   Annual Review of Pathology-Mechanisms of Disease