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nature portfolio privacy policy advertising social media cambridge research institute oestrogen-receptor-positive health research awards canada research chair reprints nature methods 5 development nature genet principal rna-editing enzymes health research centrosome-independent microtubule generation aligned paired-end sequence nature 456 nature 446 nature 452 nature 461 nature unequal segmental amplification/deletion cbcf bc/yukon chapter ttr-breast tumour bank integrating rna-seq data wtss library sequence low-intermediate histological grade supplementary figures s1-s9 rna-seq library commercial-share alike licence michael smith foundation synonymous variants/deletions affecting permissions synonymous transcript editing rna-editing enzymes author contributions original author samuel aparicio potential editing events prognostic model based generation sequencing approaches synonymous editing positions rna-editing events supplementary tables s1-s12 accession number egas00000000054 editing enzyme expressed single nucleotide resolution transcriptome data revealed advanced breast cancer privacy

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         headline:Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
         description:Next-generation sequencing approaches have been used to investigate the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer from a patient — rather than from a cell line or xenograft — over a 9-year period between the diagnosis of the primary tumour and the appearance of metastasis. Comparison of the somatic non-synonymous coding mutations in the metastasis and the primary tumour of the same patient and the combined analysis of genome and transcriptome data provided insights into the mutational evolution that can occur with disease progression. The cover shows sequence elements of the HAUS3 locus, one of the genes found to be mutated in the tissue (shown in the background) from the primary lobular cancer used for this work. Advances in next generation sequencing have made it possible to precisely characterize the coding mutations that occur during the development and progression of individual cancers. Here, this technique is used to sequence the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer; significant evolution is found to occur with disease progression. Recent advances in next generation sequencing1,2,3,4 have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1–13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.
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ScholarlyArticle:
      headline:Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
      description:Next-generation sequencing approaches have been used to investigate the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer from a patient — rather than from a cell line or xenograft — over a 9-year period between the diagnosis of the primary tumour and the appearance of metastasis. Comparison of the somatic non-synonymous coding mutations in the metastasis and the primary tumour of the same patient and the combined analysis of genome and transcriptome data provided insights into the mutational evolution that can occur with disease progression. The cover shows sequence elements of the HAUS3 locus, one of the genes found to be mutated in the tissue (shown in the background) from the primary lobular cancer used for this work. Advances in next generation sequencing have made it possible to precisely characterize the coding mutations that occur during the development and progression of individual cancers. Here, this technique is used to sequence the genomes and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer; significant evolution is found to occur with disease progression. Recent advances in next generation sequencing1,2,3,4 have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-α-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1–13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.
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      keywords:
         Science
         Humanities and Social Sciences
         multidisciplinary
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            address:
               name:Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada ,
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            address:
               name:Deeley Research Centre, BC Cancer Agency, Victoria V8R 6V5, Canada
               type:PostalAddress
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            address:
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               type:PostalAddress
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            name:University of British Columbia, G227-2211 Wesbrook Mall, British Columbia, Vancouver V6T 2B5, Canada
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            address:
               name:Michael Smith Genome Sciences Centre, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada ,
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            address:
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