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Article
Gene prioritization through genomic data fusion
The identification of genes involved in health and disease remains a challenge. We describe a bioinformatics approach, together with a freely accessible, interactive and flexible software termed Endeavour, to ...
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Article
Erratum: Gene prioritization through genomic data fusion
Nat. Biotechnol. 24, 537–544 (2006) In the print version of this article and the version originally published online, reference 5 was mistakenly included on page 537, column 2, lines 3, 10 and reference 1 on l...
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Article
Open AccessModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and...
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Article
Open AccessCollaboratively charting the gene-to-phenotype network of human congenital heart defects
How to efficiently integrate the daily practice of molecular biologists, geneticists, and clinicians with the emerging computational strategies from systems biology is still much of an open question.
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Protocol
Analyzing Cancer Samples with SNP Arrays
Single nucleotide polymorphism (SNP) arrays are powerful tools to delineate genomic aberrations in cancer genomes. However, the analysis of these SNP array data of cancer samples is complicated by three phenom...
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Article
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Data filters separate true genetic variants in sequencing data from sequencing errors, but their effectiveness is difficult to assess. Reumers et al. use the genome sequences of monozygotic twins to evaluate the ...
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Article
The landscape of cancer genes and mutational processes in breast cancer
A study of breast cancers shows that the number of somatic mutations in each varies markedly and is strongly correlated with age at diagnosis and cancer histological grade.
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Article
ABSOLUTE cancer genomics
Calculating absolute copy numbers in cancer genome sequences identifies disease-associated genes and provides insights into tumor evolution and heterogeneity.
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Article
Open AccessCopynumber: Efficient algorithms for single- and multi-track copy number segmentation
Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, ...
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Article
Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma
Andrew Futreal and colleagues identify the major cartilage collagen gene COL2A1 as a frequent target of somatic mutation in chondrosarcoma. The mutation patterns are consistent with selection for variants likely ...
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Article
Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone
Adrienne Flanagan and colleagues identify distinct driver mutations in H3F3A and H3F3B in chondroblastoma and giant cell tumor of bone. The mutations occur in over 90% of tumors and exhibit a high degree of tumor...
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Article
Open AccessThe genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models
Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even...
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Article
Open AccessHeterogeneity of genomic evolution and mutational profiles in multiple myeloma
Multiple myeloma is an incurable plasma cell malignancy with a complex and incompletely understood molecular pathogenesis. Here we use whole-exome sequencing, copy-number profiling and cytogenetics to analyse ...
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Article
RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia
Peter Campbell, Mel Greaves and colleagues use exome and whole-genome sequencing to characterize somatic mutations in childhood acute lymphoblastic leukemias with the ETV6-RUNX1 fusion gene. They find that RAG-me...
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Article
Correction: Corrigendum: Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone
Nat. Genet. 45, 1479–1482 (2013); published online 27 October 2013; corrected after print 6 February 2014 In the version of this article initially published, the name of author Victoria Goody was misspelled, a...
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Article
Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia
A rare constitutional translocation between chromosomes 15 and 21 predisposes to catastrophic chromosomal damage followed by amplification of megabase regions, causing a specific subtype of acute lymphoblastic...
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Article
Recurrent PTPRB and PLCG1 mutations in angiosarcoma
Peter Campbell and colleagues identify PLCG1 and PTPRB as new driver genes for angiosarcoma through whole-exome sequencing of tumor samples. They find somatic PTPRB mutations in 10 of 39 cases and PLCG1 mutations...
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Article
Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers
Adam Shlien, Peter Campbell, Uri Tabori and colleagues report genome and exome sequencing of biallelic mismatch repair deficiency cancer samples from 12 children, including 10 high-grade gliomas. The hypermuta...
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Article
Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue
Colin Cooper and colleagues report genome-wide sequences of multiple samples of multifocal cancer and morphologically normal tissue from the prostates of three men. They found high levels of mutations in morph...
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Article
The evolutionary history of lethal metastatic prostate cancer
The subclonal composition of human prostate tumours and their metastases has been mapped by whole-genome sequencing, thus establishing the evolutionary trees behind the development and spread of these cancers...
