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Article
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine
Whole-exome sequencing (WES) has emerged as a transformative technology for biological discovery, but technical difficulties have so far prevented its widespread clinical use. Here, Eliezer Van Allen and colle...
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Article
Correction: Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples
Nat. Methods 10, 623–629 (2013); published online 19 May 2013; corrected after 2 December 2013 In the version of this article initially published, in the Online Methods “RNase H libraries” section, the sentenc...
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Article
Somatic mutation of CDKN1B in small intestine neuroendocrine tumors
Matthew Meyerson and colleagues report whole-exome and whole-genome sequencing of 55 small intestine neuroendocrine tumors. They identify recurrent somatic mutations in CDKN1B, implicating cell cycle dysregulatio...
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Article
Comparative analysis of RNA sequencing methods for degraded or low-input samples
This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.
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Article
Mutational heterogeneity in cancer and the search for new cancer-associated genes
As the sample size in cancer genome studies increases, the list of genes identified as significantly mutated is likely to include more false positives; here, this problem is identified as stemming largely from...
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Article
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
Adam Bass, Gad Getz and colleagues report whole-exome sequencing of 149 esophageal adenocarcinomas (EACs) and whole-genome sequencing of 15 EACs. They identify a mutational signature defined by a high prevalen...
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Article
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
The MuTect algorithm for calling somatic point mutations enables subclonal analysis of the whole-genome or whole-exome sequencing data being generated in large-scale cancer genomics projects.
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Article
The genetic landscape of high-risk neuroblastoma
John Maris, Matthew Meyerson, Marco Marra and colleagues report results of a large-scale sequencing study of neuroblastoma. They observe a low median exonic mutation frequency and strikingly few recurrently mu...
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Article
Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations
Medulloblastoma is the most common brain tumour in children; using exome sequencing of tumour samples the authors show that these cancers have low mutation rates and identify 12 significantly mutated genes, am...
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Article
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
Levi Garraway and colleagues report exome sequencing of 112 prostate adenocarcinomas and matched normal tissues. They identify novel recurrent mutations in several genes, including MED12, FOXA1 and SPOP. They fin...
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Article
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
Matthew Meyerson and colleagues report the whole-genome sequencing of primary colorectal tumors and matched adjacent non-tumor tissue from nine individuals with colorectal cancer. They identify a recurrent VTI1A-...
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Article
RNA-Seq methods for imperfect samples: development, evaluation and applications
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Article
RNA-Seq methods for imperfect samples: development, evaluation and applications
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Article
Open AccessInitial genome sequencing and analysis of multiple myeloma
Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched nor...
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Article
Genome-scale DNA methylation maps of pluripotent and differentiated cells
DNA methylation, an important mechanism of epigenetic modification that produces different patterns of gene expression from a single DNA sequence, is vital to normal development and its malfunction can cause c...
