Tumor Genome Sequencing
  • Widespread Genetic Heterogeneity in Multiple Myeloma: Implications for Targeted Therapy (203 samples).
    Cancer Cell, 10.1016/j.ccr.2013.12.015, 2014, peper link
  • Landscape of genomic alterations in cervical carcinomas (115 samples).
    Nature, doi:10.1038/nature12881, 2014, peper link
  • Somatic mutation of CDKN1B in small intestine neuroendocrine tumors (50 samples).
    Nature Genet, doi:10.1038/ng.2821, 2013, peper link
  • Exome sequencing identifies distinct mutational patterns in liver fluke–related and non-infection-related bile duct cancers (15 + 194 samples).
    Nature Genet, doi:10.1038/ng.2806, 2013, peper link
  • Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas (32 samples).
    Nature Genet, doi:10.1038/ng.2813, 2013, peper link
  • Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy (17 + 60 samples, survival).
    Nature Genet, doi:10.1038/ng.2799, 2013, peper link
  • Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation (99 samples, survival).
    Nature Genet, doi:10.1038/ng.2798, 2013, peper link
  • Frequent truncating mutations of STAG2 in bladder cancer .
    Nature Genet, doi:10.1038/ng.2800, 2013, peper link
  • The Somatic Genomic Landscape of Glioblastoma (291+42 samples).
    Cell, http://dx.doi.org/10.1016/j.cell.2013.09.034, 2013, peper link
  • Integrated molecular analysis of clear-cell renal cell carcinoma (106 samples, survival).
    Nature Genet, doi:10.1038/ng.2699, 2013, peper link
  • Somatic SETBP1 mutations in myeloid malignancies (20 samples, survival, WGS).
    Nature Genet, doi:10.1038/ng.2696, 2013, peper link
  • Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia (13 samples, survival).
    Nature Genet, doi:10.1038/ng.2698, 2013, peper link
  • Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma (96 samples, WGS).
    Nature Genet, doi:10.1038/ng.2682, 2013, peper link
  • Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma (49 samples).
    Nature Genet, doi:10.1038/ng.2668, 2013, peper link
  • The mutational landscape of adenoid cystic carcinoma (salivary gland cancers) (60 samples, WGS).
    Nature Genet, doi:10.1038/ng.2643, 2013, peper link
  • Comprehensive molecular characterization of clear cell renal cell carcinoma (417, survival).
    Nature, doi:10.1038/nature12222, 2013, peper link
  • Whole genome sequencing identifies recurrent mutations in hepatocellular carcinoma (88 samples, survival).
    Genome Research, doi: 10.1101/gr.154492.113, 2013, peper link
  • Genome Evolution during Progression to Breast Cancer (6 samples).
    Genome Research, doi: 10.1101/gr.151670.112, 2013, peper link
  • Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas (151 samples).
    Nature Genet, doi:10.1038/ng.2611, 2013, peper link
  • Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA (Plasma/CTC).
    Nature, doi:10.1038/nature12065, 2013, peper link
  • Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes (140 samples).
    Cell, http://dx.doi.org/10.1016/j.cell.2013.04.010, 2013, peper link
  • Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia (200 samples including 50 WGS).
    NEJM, DOI: 10.1056/NEJMoa1301689, 2013, peper link
  • Punctuated Evolution of Prostate Cancer Genomes (57 samples, Clonal evo).
    Cell, http://dx.doi.org/10.1016/j.cell.2013.03.021, 2013, peper link
  • Integrated genomic characterization of endometrial carcinoma (373 samples, survival).
    Nature, doi:10.1038/nature12113, 2013, peper link
  • Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity (149 samples, 30X).
    Nat Genet, doi:10.1038/ng.2591, 2013, peper link
  • Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia (149 samples, >100X).
    Cell, http://dx.doi.org/10.1016/j.cell.2013.01.019, 2013, peper link
  • Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer (17 samples - age-dependent).
    Cancer Cell, 10.1016/j.ccr.2013.01.002, 2013, peper link
  • Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia (67 samples).
    Nature Genet, doi:10.1038/ng.2508, 2013, peper link
  • Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas (family).
    Nature Genet, doi:10.1038/ng.2503, 2013, peper link
2012
  • The genetic landscape of mutations in Burkitt lymphoma (59 samples).
    Nature Genet, doi:10.1038/ng.2468, 2012, peper link
  • The transcriptional landscape and mutational profile of lung adenocarcinoma (87 samples).
    Genome Research, 2012, peper link
  • Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes (142 samples).
    Nature, doi:10.1038/nature11547, 2012, peper link
  • Exome sequencing of hepatitis B virus–associated hepatocellular carcinoma (10 samples).
    Nature Genetics, doi:10.1038/ng.2391, 2012, peper link
  • Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer (31 samples).
    Nature Genetics, doi:10.1038/ng.2396, 2012, peper link
  • Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer (53 samples, 16 cell lines).
    Nature Genetics, doi:10.1038/ng.2405, 2012, peper link
  • Comprehensive molecular portraits of human breast tumours (825 samples, survival).
    Nature, doi:10.1038/nature11412, 2012, peper link
  • Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers (17 samples).
    Cell, 10.1016/j.cell.2012.08.024, 2012, peper link
  • Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing (183 samples).
    Cell, 10.1016/j.cell.2012.08.029, 2012, peper link
  • Comprehensive genomic characterization of squamous cell lung cancers (178 samples).
    Nature, doi:10.1038/nature11404, 2012, peper link
  • Novel mutations target distinct subgroups of medulloblastoma (37 samples).
    Nature, doi:10.1038/nature11213, 2012, peper link
  • Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations (92 samples).
    Nature, doi:10.1038/nature11329, 2012, peper link
  • Dissecting the genomic complexity underlying medulloblastoma (125 samples).
    Nature, doi:10.1038/nature11284, 2012, peper link
  • The Origin and Evolution of Mutations in Acute Myeloid Leukemia (24 samples).
    Cell, 10.1016/j.cell.2012.06.023, 2012, peper link
  • A Landscape of Driver Mutations in Melanoma (121 samples).
    Cell, 10.1016/j.cell.2012.06.024, 2012, peper link
  • Comprehensive molecular characterization of human colon and rectal cancer (224 samples, survival).
    Nature, doi:10.1038/nature11252, 2012, peper link
  • Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators (27 samples).
    Nature Genetics, doi:10.1038/ng.2291, 2012, peper link
  • BAP1 loss defines a new class of renal cell carcinoma (8 samples).
    Nature Genetics, doi:10.1038/ng.2323, 2012, peper link
  • Sequence analysis of mutations and translocations across breast cancer subtypes (125 samples).
    Nature, doi:10.1038/nature11154, 2012, peper link
  • Novel mutations target distinct subgroups of medulloblastoma (37 samples).
    Nature, doi:10.1038/nature11213, 2012, peper link
  • Whole-genome analysis informs breast cancer response to aromatase inhibition (77 samples).
    Nature, doi:10.1038/nature11143, 2012, peper link
  • The Pediatric Cancer Genome Projectr (206 - 600 samples).
    Nature Genetics, doi:10.1038/ng.2287, 2012, peper link
  • Exome sequencing of liver fluke, associated cholangiocarcinoma (8 samples).
    Nature Genetics, doi:10.1038/ng.2273, 2012, peper link
  • Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma (24 samples).
    Nature Genetics, doi:10.1038/ng.2256, 2012, peper link
  • Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer (112 samples).
    Nature Genetics, doi:10.1038/ng.2279, 2012, peper link
  • The mutational landscape of lethal castration-resistant prostate cancer (50 samples, drug treated).
    Nature, doi:10.1038/nature11125, 2012, peper link
  • The Life History of 21 Breast Cancers (21 samples, whole genome).
    Cell, 10.1016/j.cell.2012.04.023, 2012, peper link
  • The landscape of cancer genes and mutational processes in breast cancer (100 samples).
    Nature, doi:10.1038/nature11017, 2012, peper link
  • Melanoma genome sequencing reveals frequent PREX2 mutations (25 samples).
    Nature, doi:10.1038/nature11071, 2012, peper link
  • Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes (15 samples).
    Nature Genet, doi:10.1038/ng.2246, 2012, peper link
  • The clonal and mutational evolution spectrum of primary triple-negative breast cancers (65 samples).
    Nature, doi:10.1038/nature10933, 2012, peper link
  • Clonal Architecture of Secondary Acute Myeloid Leukemia (7 samples).
    N Engl J Med, 366:1090-1098, 2012, peper link
  • Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing (cut into piceses).
    N Engl J Med, 366:883-892, 2012, peper link
  • Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting.
    Nature, doi:10.1038/nature10755, 2012, peper link
  • Discovery and prioritization of somatic mutations in DLBCL by whole-exome sequencing (55 samples).
    PNAS, doi: 10.1073/pnas.1121343109, 2012, peper link
  • Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma (48 samples).
    Nature, doi:10.1038/nature10833, 2012, peper link
  • The genetic basis of early T-cell precursor acute lymphoblastic leukaemia (12 samples).
    Nature, doi:10.1038/nature10725, 2012, peper link
  • Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencinga (8 samples).
    Nature, doi:10.1038/nature10738, 2012, peper link
  • Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas (7 samples).
    Nature Genet, doi:10.1038/ng.1102, 2012, peper link
  • Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma (7 lines).
    Nature Genet, doi:10.1038/ng.1026, 2012, peper link
  • Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing (8 lines).
    Nature Genet, doi:10.1038/ng.1041, 2012, peper link
  • Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency (15 lines).
    Genome Res, 22:208-219, 2012, peper link
  • Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia (105 samples).
    Nature Genet, doi:10.1038/ng.1032, 2012, peper link
2011
  • Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer (22 samples).
    Nature Genet, doi:10.1038/ng.982, 2011, peper link
  • Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma (11 samples).
    Nature Genet, doi:10.1038/ng.950, 2011, peper link
  • Analysis of the coding genome of diffuse large B-cell lymphoma (6 samples).
    Nature Genet, doi:10.1038/ng.892, 2011, peper link
  • Exome sequencing identifies GRIN2A as frequently mutated in melanoma (14 samples).
    Nature Genet, doi:10.1038/ng.810, 2011, peper link
  • Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia (9 samples).
    Nature Genet, doi:10.1038/ng.788, 2011, peper link
  • Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma (13 samples).
    Nature, doi:10.1038/nature10351, 2011, peper link
  • Integrated genomic analyses of ovarian carcinoma (316 samples) .
    Nature, doi:10.1038/nature10166, 2011, peper link
  • Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers (23 samples).
    PNAS, doi: 10.1073/pnas.1108745108, 2011, peper link
  • Exome Sequencing Reveals Comprehensive Genomic Alterations across Eight Cancer Cell Lines (8 cell lines).
    PLoS One, 6: e21097, 2011, peper link
  • Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia (4 samples).
    Nature, doi:10.1038/nature10113, 2011, peper link
  • Initial genome sequencing and analysis of multiple myeloma (38 samples).
    Nature, doi:10.1038/nature09837, 2011, peper link
  • Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma (7 samples).
    Nature, doi:10.1038/nature09639, 2011, peper link
  • The mutational landscape of head and neck squamous cell carcinoma (74 samples).
    Science, 333: 1157-1160, 2011, peper link
  • Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1 (32 samples).
    Science, 333: 1154-1157, 2011, peper link
  • Mutations in CIC and FUBP1 Contribute to Human Oligodendroglioma (7 samples).
    Science, 333:1453-1455, 2011, peper link
2010
  • Distant metastasis occurs late during the genetic evolution of pancreatic cancer.
    Nature, doi:10.1038/nature09515, 2010, peper link
  • DNMT3A Mutations in Acute Myeloid Leukemia.
    N Engl J Med, 363:2424-2433, 2010, peper link
  • Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations.
    Nature, doi:10.1038/nature09327, 2010, peper link
  • Diverse somatic mutation patterns and pathway alterations in human cancers (1,500 genes X 441 samples).
    Nature, doi:10.1038/nature09208, 2010, peper link