A new era of long-read sequencing for cancer genomics

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

(2019) Melissa Leija-Salazar et al.   Molecular Genetics & Genomic Medicine

Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

(2019) Daniel P. Depledge et al.   Nature Communications

Using long-read sequencing to detect imprinted DNA methylation

(2019) Scott Gigante et al.   NUCLEIC ACIDS RESEARCH

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing

(2018) Srinivas R. Viswanathan et al.   CELL

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

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

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Accurate detection of complex structural variations using single-molecule sequencing

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

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

(2018) Tslil Gabrieli et al.   NUCLEIC ACIDS RESEARCH

Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines

(2018) Sarun Sereewattanawoot et al.   Scientific Reports

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

(2018) Haotian Teng et al.   GigaScience

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

(2018) Roger Volden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia

(2018) Paola Orsini et al.   Scientific Reports

Evaluation and application of RNA-Seq by MinION

(2018) Masahide Seki et al.   DNA RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control

(2017) Isaia Barbieri et al.   NATURE

Graphtyper enables population-scale genotyping using pangenome graphs

(2017) Hannes P Eggertsson et al.   NATURE GENETICS

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

DBTSS/DBKERO for integrated analysis of transcriptional regulation

(2017) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases

(2017) Stephanie U. Greer et al.   Genome Medicine

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

(2016) Matei David et al.   BIOINFORMATICS

Nanopore sequencing detects structural variants in cancer

(2016) Alexis L. Norris et al.   CANCER BIOLOGY & THERAPY

TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

(2016) Crescenzio Francesco Minervini et al.   Diagnostic Pathology

The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

(2016) Shuibin Lin et al.   MOLECULAR CELL

Aberrant PD-L1 expression through 3′-UTR disruption in multiple cancers

(2016) Keisuke Kataoka et al.   NATURE

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

Osimertinib in the treatment of patients with epidermal growth factor receptor T790M mutation-positive metastatic non-small cell lung cancer: clinical trial evidence and experience

(2016) Ivana Sullivan et al.   Therapeutic Advances in Respiratory Disease

Allele-Specific Quantification of Structural Variations in Cancer Genomes

(2016) Yang Li et al.   Cell Systems

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)

(2015) Yao Yang et al.   BMC GENOMICS

The Allelic Context of the C797S Mutation Acquired upon Treatment with Third-Generation EGFR Inhibitors Impacts Sensitivity to Subsequent Treatment Strategies

(2015) M. J. Niederst et al.   CLINICAL CANCER RESEARCH

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

(2015) Wenjun Jiang et al.   Nature Communications

TERT promoter mutations and monoallelic activation of TERT in cancer

(2015) F W Huang et al.   Oncogenesis

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Acquired resistance to TKIs in solid tumours: learning from lung cancer

(2014) D. Ross Camidge et al.   Nature Reviews Clinical Oncology

Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines

(2014) Ayako Suzuki et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

RETfusion gene: Translation to personalized lung cancer therapy

(2013) Takashi Kohno et al.   CANCER SCIENCE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS