Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA

[1]  Trevor J Pugh,et al.  Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab , 2020, Nature Cancer.

[2]  N. Rosenfeld,et al.  ctDNA monitoring using patient-specific sequencing and integration of variant reads , 2020, Science Translational Medicine.

[3]  Ash A. Alizadeh,et al.  Integrating genomic features for non-invasive early lung cancer detection , 2020, Nature.

[4]  The Icgctcga Pan-Cancer Analysis of Whole Genomes Consortium.  Pan-cancer analysis of whole genomes , 2020 .

[5]  Nuno A. Fonseca,et al.  Patterns of somatic structural variation in human cancer genomes , 2020, Nature.

[6]  Ash A. Alizadeh,et al.  Circulating tumor DNA dynamics predict benefit from consolidation immunotherapy in locally advanced non-small-cell lung cancer , 2020, Nature Cancer.

[7]  David R. Jones,et al.  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants , 2019, Nature Medicine.

[8]  S. Shchegrova,et al.  Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer , 2019, JAMA oncology.

[9]  Ash A. Alizadeh,et al.  Reply to J. Wang et al. , 2019, Journal of Clinical Oncology.

[10]  Ash A. Alizadeh,et al.  Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma. , 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[11]  Christopher T. Saunders,et al.  Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.

[12]  Charles Swanton,et al.  Early stage NSCLC — challenges to implementing ctDNA-based screening and MRD detection , 2018, Nature Reviews Clinical Oncology.

[13]  Ville Mustonen,et al.  The repertoire of mutational signatures in human cancer , 2018, Nature.

[14]  Roland Schmitz,et al.  Genetics and Pathogenesis of Diffuse Large B‐Cell Lymphoma , 2018, The New England journal of medicine.

[15]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[16]  Daniel A. Haber,et al.  Cancer detection: Seeking signals in blood , 2018, Science.

[17]  R. Levy,et al.  Axicabtagene Ciloleucel CAR T‐Cell Therapy in Refractory Large B‐Cell Lymphoma , 2017, The New England journal of medicine.

[18]  Sam Angiuoli,et al.  Direct detection of early-stage cancers using circulating tumor DNA , 2017, Science Translational Medicine.

[19]  Ashwini Naik,et al.  Phylogenetic ctDNA analysis depicts early stage lung cancer evolution , 2017, Nature.

[20]  F. Diehl,et al.  Performance of Streck cfDNA Blood Collection Tubes for Liquid Biopsy Testing , 2016, PloS one.

[21]  Ash A. Alizadeh,et al.  Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA , 2016, Science Translational Medicine.

[22]  R. Strausberg,et al.  Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer , 2016, Science Translational Medicine.

[23]  Ash A. Alizadeh,et al.  Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients , 2016, Nature Communications.

[24]  M. Lieber.  Mechanisms of human lymphoid chromosomal translocations , 2016, Nature Reviews Cancer.

[25]  Ash A. Alizadeh,et al.  Integrated digital error suppression for improved detection of circulating tumor DNA , 2016, Nature Biotechnology.

[26]  B. Taylor,et al.  deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution , 2016, Genome Biology.

[27]  M. Stratton,et al.  Clock-like mutational processes in human somatic cells , 2015, Nature Genetics.

[28]  Jorge S. Reis-Filho,et al.  Mutation tracking in circulating tumor DNA predicts relapse in early breast cancer , 2015, Science Translational Medicine.

[29]  A. Valencia,et al.  Non-coding recurrent mutations in chronic lymphocytic leukaemia , 2015, Nature.

[30]  L. Staudt,et al.  Circulating tumour DNA and CT monitoring in patients with untreated diffuse large B-cell lymphoma: a correlative biomarker study. , 2015, The Lancet. Oncology.

[31]  V. Wong,et al.  Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients , 2015, Proceedings of the National Academy of Sciences.

[32]  Yijun Ruan,et al.  B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity , 2014, Cell.

[33]  Brendan F. Kohrn,et al.  Detecting ultralow-frequency mutations by Duplex Sequencing , 2014, Nature Protocols.

[34]  Franck Molina,et al.  Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA , 2014, Nature Medicine.

[35]  M. Choti,et al.  Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies , 2014, Science Translational Medicine.

[36]  Ash A. Alizadeh,et al.  An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage , 2013, Nature Medicine.

[37]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[38]  Steven J. M. Jones,et al.  Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. , 2013, Blood.

[39]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[40]  N. A. Temiz,et al.  Evidence for APOBEC3B mutagenesis in multiple human cancers , 2013, Nature Genetics.

[41]  Takashi Akasaka,et al.  BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements. , 2013, Blood.

[42]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[43]  G. Parmigiani,et al.  Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[44]  R. Spang,et al.  Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing , 2012, Nature Genetics.

[45]  Steven J. M. Jones,et al.  Recurrent targets of aberrant somatic hypermutation in lymphoma , 2012, Oncotarget.

[46]  L. Staudt,et al.  Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics , 2012, Nature.

[47]  Jesse J. Salk,et al.  Detection of ultra-rare mutations by next-generation sequencing , 2012, Proceedings of the National Academy of Sciences.

[48]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[49]  Raul Rabadan,et al.  Analysis of the Coding Genome of Diffuse Large B-Cell Lymphoma , 2011, Nature Genetics.

[50]  Steven J. M. Jones,et al.  MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers , 2011, Nature.

[51]  Francisco M. De La Vega,et al.  Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing , 2010, Science Translational Medicine.

[52]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[53]  M. Nussenzweig,et al.  AID Is Required for the Chromosomal Breaks in c-myc that Lead to c-myc/IgH Translocations , 2008, Cell.

[54]  L. Staudt,et al.  Aberrant immunoglobulin class switch recombination and switch translocations in activated B cell–like diffuse large B cell lymphoma , 2007, The Journal of experimental medicine.

[55]  A. Ramiro,et al.  Activation-induced deaminase: light and dark sides. , 2006, Trends in molecular medicine.

[56]  F. Cohen,et al.  Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray , 2003, Genome Biology.

[57]  Gouri Nanjangud,et al.  Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas , 2001, Nature.

[58]  L. Mariani,et al.  Analysis of circulating tumor DNA in plasma at diagnosis and during follow-up of lung cancer patients. , 2001, Cancer research.

[59]  N. Nakamura,et al.  Analysis of the immunoglobulin heavy chain gene variable region of CD5-positive and -negative diffuse large B cell lymphoma , 2001, Leukemia.

[60]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[61]  N. Sugimoto,et al.  Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. , 1996, Nucleic acids research.

[62]  D. Turner,et al.  Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[63]  J. Rowley.  Chromosome studies in the non-Hodgkin's lymphomas: the role of the 14;18 translocation. , 1988, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[64]  S. Goodman,et al.  Circulating mutant DNA to assess tumor dynamics , 2008, Nature Medicine.