Genome Medicine | All articles

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Medicine

Advertisement

Articles

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
		Method Multiplex target capture with double-stranded DNA probes Peidong Shen, Wenyi Wang, Aung-Kyaw Chi, Yu Fan, Ronald W Davis, Curt Scharfe Genome Medicine 2013, 5:50 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An approach to enrich for regions of interest in the DNA, using complementary long padlock probes, shows improved accuracy and target coverage and potentially lower cost than previous methods.
		Research Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors Matthias Lechner, Garrett Frampton, Tim Fenton, Andrew Feber, Gary Palmer, Amrita Jay, Nischalan Pillay, Martin Forster, Maureen T Cronin, Doron Lipson, Vincent A Miller, Timothy A Brennan, Stephen Henderson, Francis Vaz, Paul O’Flynn, Nicholas Kalavrezos, Roman Yelenski, Stephan Beck, Philip J Stephens, Chris Boshoff Genome Medicine 2013, 5:49 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Next-generation sequencing of head and neck squamous cell carcinoma uncovers genetic alterations in HPV+ and HPV- tumors, suggesting a causal role for HPV in this cancer.
		Review Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics Dan A Landau, Catherine J Wu Genome Medicine 2013, 5:47 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Catherine Wu and Dan Landau review genomic studies of chronic lymphocytic leukemia, which have revealed genetic and epigenetic heterogeneity, and mutations associated with poor prognosis.
		Research highlight Improved coverage and accuracy with strand-conserving sequence enrichment Toumy Guettouche, Stephan Zuchner Genome Medicine 2013, 5:46 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Stephan Zuchner and Toumy Guettouche discuss the advantages of a recently published approach for target sequence enrichment to be used in clinical diagnosis and highlight potential new applications.
		Review Genome-wide approaches for identifying genetic risk factors for osteoporosis Shuyan Wu, Yongjun Liu, Lei Zhang, Yingying Han, Yong Lin, Hong-Wen Deng Genome Medicine 2013, 5:44 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hong-Wen Deng and colleagues review genome-wide approaches for identifying risk factors for osteoporosis, including genome-wide association, gene expression profiling and proteomic studies.
		Meeting report Genomic disorders: complexity at multiple levels Santhosh Girirajan Genome Medicine 2013, 5:43 (29 May 2013) Abstract \| Full text \| PDF \| PubMed
		Musings Hunting for cancer in the microbial jungle Pauline Funchain, Charis Eng Genome Medicine 2013, 5:42 (29 May 2013) Abstract \| Full text \| PDF \| Editor’s summary Charis Eng and Pauline Funchain ponder the roles of microbial diversity and microbial profiling in cancer, and consider the prospects of hunting for cancer and its causes amidst the wildlife of the human microbiome.
		Research Genes and pathways underlying regional and cell type changes in Alzheimer's disease Jeremy A Miller, Randall L Woltjer, Jeff M Goodenbour, Steve Horvath, Daniel H Geschwind Genome Medicine 2013, 5:48 (25 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Transcriptomic and systems analyses of two brain regions in Alzheimer's disease reveals associations between disease status, transcript levels, and brain region.
		Research Survey of European clinical geneticists on awareness, experiences and attitudes towards direct-to-consumer genetic testing Heidi Carmen Howard, Pascal Borry Genome Medicine 2013, 5:45 (22 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An online survey of European clinical geneticists found high awareness of direct-to-consumer genetic testing but most participants did not agree with such testing for severe conditions.
		Musings Expression profiling: a cost-effective biomarker discovery tool for the personal genome era David Gurwitz Genome Medicine 2013, 5:41 (14 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Gurwitz argues that expression profiling is currently the most promising and cost-effective tool for discovery of new prognostic, diagnostic and therapeutic biomarkers.
		Research An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype John W Whitaker, Robert Shoemaker, David L Boyle, Josh Hillman, David Anderson, Wei Wang, Gary S Firestein Genome Medicine 2013, 5:40 (30 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Key genes in cultured rheumatoid arthritis cells are stably differentially methylated compared to osteoarthritis or normal cells, and are potential therapeutic targets.
		Review Protein-protein interaction networks: probing disease mechanisms using model systems Uros Kuzmanov, Andrew Emili Genome Medicine 2013, 5:37 (30 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Kuzmanov and Emili review recent advances in protein-protein interaction studies from various model organisms, shedding light on the mechanisms and possible treatments for human disease.
		Musings The Human Genome Organisation: towards next-generation ethics Bartha Knoppers, Adrian Thorogood, Ruth Chadwick Genome Medicine 2013, 5:38 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Knoppers, Thorogood and Chadwick muse over the evolution of ethical statements and policy over the course of the human genome project and beyond, marking 10 years since its completion.
		Review Genomics and outbreak investigation: from sequence to consequence Esther R Robinson, Timothy M Walker, Mark J Pallen Genome Medicine 2013, 5:36 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Pallen and co-authors review advances in applying high-throughput sequencing approaches for outbreak investigation (focusing on bacterial infections), and discuss the implications for clinical microbiology.
		Research highlight Plasma-seq: a novel strategy for metastatic prostate cancer analysis Caitlin Farris, Jeffrey M Trimarchi Genome Medicine 2013, 5:35 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Caitlin Farris and Jeffrey Trimarchi discuss how a new non-invasive approach for personalized diagnosis of prostate cancer shows promise for the clinic, being both time- and cost-effective.
		Review The genomics of preterm birth: from animal models to human studies Katherine Y Bezold, Minna K Karjalainen, Mikko Hallman, Kari Teramo, Louis J Muglia Genome Medicine 2013, 5:34 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Louis Muglia and colleagues review the genetics and genomics of pre-term birth and birth timing, discussing the limitations of animal models and the progress of human studies.
		Method Development and validation of a robust automated analysis of plasma phospholipid fatty acids for metabolic phenotyping of large epidemiological studies Laura Wang, Keith Summerhill, Carmen Rodriguez-Canas, Ian Mather, Pinal Patel, Michael Eiden, Stephen Young, Nita G Forouhi, Albert Koulman Genome Medicine 2013, 5:39 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fully automated high-throughput method provides proof-of-concept that fatty acid profiling of human plasma is achievable for metabolic phenotyping in large epidemiological and genetic studies.
		Musings Are randomized trials obsolete or more important than ever in the genomic era? John PA Ioannidis, Muin J Khoury Genome Medicine 2013, 5:32 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Ioannidis and Muin Khoury reflect on how advances in the field of genomics are questioning the need for randomized clinical trials and revolutionizing their design.
		Editorial Microbial genomics: an increasingly revealing interface in human health and disease Martin L Hibberd Genome Medicine 2013, 5:31 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Guest Editor Martin Hibberd highlights advances in genomics, metagenomics and other high-throughput approaches for studying human-microbe interactions in health and disease, and the applications for medicine.
		Research Isoform level expression profiles provide better cancer signatures than gene level expression profiles ZhongFa Zhang, Sharmistha Pal, Yingtao Bi, Julia Tchou, Ramana V Davuluri Genome Medicine 2013, 5:33 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Expression profiles at the isoform level perform better than those at the gene level to discriminate between cancer cell lines and non-oncogenic cells, regardless of tissue of origin.
		Research Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing Ellen Heitzer, Peter Ulz, Jelena Belic, Stefan Gutschi, Franz Quehenberger, Katja Fischereder, Theresa Benezeder, Martina Auer, Carina Pischler, Sebastian Mannweiler, Martin Pichler, Florian Eisner, Martin Haeusler, Sabine Riethdorf, Klaus Pantel, Hellmut Samonigg, Gerald Hoefler, Herbert Augustin, Jochen B Geigl, Michael R Speicher Genome Medicine 2013, 5:30 (5 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic monitoring of prostate cancer using non-invasive plasma DNA sequencing can be carried out quickly and cheaply using a benchtop high-throughput sequencer.
		Method Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction Gerald Quon, Syed Haider, Amit G Deshwar, Ang Cui, Paul C Boutros, Quaid Morris Genome Medicine 2013, 5:29 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The ISOpure algorithm generates a sample-specific gene expression profile, from which the impact of heterogeneous tumor composition is removed, improving prediction of clinical outcome.
		Review Pancreatic cancer genomics: insights and opportunities for clinical translation Alvin Makohon-Moore, Jacqueline A Brosnan, Christine A Iacobuzio-Donahue Genome Medicine 2013, 5:26 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Christine Iacobuzio-Donahue and colleagues review how genome sequencing is uncovering pathways involved in initiation and progression of pancreatic cancer, and the clinical implications.
		Research Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing Jason O'Rawe, Tao Jiang, Guangqing Sun, Yiyang Wu, Wei Wang, Jingchu Hu, Paul Bodily, Lifeng Tian, Hakon Hakonarson, W Evan Johnson, Zhi Wei, Kai Wang, Gholson J Lyon Genome Medicine 2013, 5:28 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Head-to-head comparison of widely used variant calling pipelines including SOAP, GATK and Complete Genomics using default parameters reveals discrepancies between the pipelines.
		Opinion Harm, hype and evidence: ELSI research and policy guidance Timothy Caulfield, Subhashini Chandrasekharan, Yann Joly, Robert Cook-Deegan Genome Medicine 2013, 5:21 (26 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Timothy Caulfield and colleagues argue that the development of policies for genomic research and medicine will be improved by efforts to incorporate evidence from ELSI research.

	All
		Method Multiplex target capture with double-stranded DNA probes Peidong Shen, Wenyi Wang, Aung-Kyaw Chi, Yu Fan, Ronald W Davis, Curt Scharfe Genome Medicine 2013, 5:50 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An approach to enrich for regions of interest in the DNA, using complementary long padlock probes, shows improved accuracy and target coverage and potentially lower cost than previous methods.
		Research Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors Matthias Lechner, Garrett Frampton, Tim Fenton, Andrew Feber, Gary Palmer, Amrita Jay, Nischalan Pillay, Martin Forster, Maureen T Cronin, Doron Lipson, Vincent A Miller, Timothy A Brennan, Stephen Henderson, Francis Vaz, Paul O’Flynn, Nicholas Kalavrezos, Roman Yelenski, Stephan Beck, Philip J Stephens, Chris Boshoff Genome Medicine 2013, 5:49 (29 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Next-generation sequencing of head and neck squamous cell carcinoma uncovers genetic alterations in HPV+ and HPV- tumors, suggesting a causal role for HPV in this cancer.
		Review Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics Dan A Landau, Catherine J Wu Genome Medicine 2013, 5:47 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Catherine Wu and Dan Landau review genomic studies of chronic lymphocytic leukemia, which have revealed genetic and epigenetic heterogeneity, and mutations associated with poor prognosis.
		Research highlight Improved coverage and accuracy with strand-conserving sequence enrichment Toumy Guettouche, Stephan Zuchner Genome Medicine 2013, 5:46 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Stephan Zuchner and Toumy Guettouche discuss the advantages of a recently published approach for target sequence enrichment to be used in clinical diagnosis and highlight potential new applications.
		Review Genome-wide approaches for identifying genetic risk factors for osteoporosis Shuyan Wu, Yongjun Liu, Lei Zhang, Yingying Han, Yong Lin, Hong-Wen Deng Genome Medicine 2013, 5:44 (29 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hong-Wen Deng and colleagues review genome-wide approaches for identifying risk factors for osteoporosis, including genome-wide association, gene expression profiling and proteomic studies.
		Meeting report Genomic disorders: complexity at multiple levels Santhosh Girirajan Genome Medicine 2013, 5:43 (29 May 2013) Abstract \| Full text \| PDF \| PubMed
		Musings Hunting for cancer in the microbial jungle Pauline Funchain, Charis Eng Genome Medicine 2013, 5:42 (29 May 2013) Abstract \| Full text \| PDF \| Editor’s summary Charis Eng and Pauline Funchain ponder the roles of microbial diversity and microbial profiling in cancer, and consider the prospects of hunting for cancer and its causes amidst the wildlife of the human microbiome.
		Research Genes and pathways underlying regional and cell type changes in Alzheimer's disease Jeremy A Miller, Randall L Woltjer, Jeff M Goodenbour, Steve Horvath, Daniel H Geschwind Genome Medicine 2013, 5:48 (25 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Transcriptomic and systems analyses of two brain regions in Alzheimer's disease reveals associations between disease status, transcript levels, and brain region.
		Research Survey of European clinical geneticists on awareness, experiences and attitudes towards direct-to-consumer genetic testing Heidi Carmen Howard, Pascal Borry Genome Medicine 2013, 5:45 (22 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An online survey of European clinical geneticists found high awareness of direct-to-consumer genetic testing but most participants did not agree with such testing for severe conditions.
		Musings Expression profiling: a cost-effective biomarker discovery tool for the personal genome era David Gurwitz Genome Medicine 2013, 5:41 (14 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Gurwitz argues that expression profiling is currently the most promising and cost-effective tool for discovery of new prognostic, diagnostic and therapeutic biomarkers.
		Research An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype John W Whitaker, Robert Shoemaker, David L Boyle, Josh Hillman, David Anderson, Wei Wang, Gary S Firestein Genome Medicine 2013, 5:40 (30 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Key genes in cultured rheumatoid arthritis cells are stably differentially methylated compared to osteoarthritis or normal cells, and are potential therapeutic targets.
		Review Protein-protein interaction networks: probing disease mechanisms using model systems Uros Kuzmanov, Andrew Emili Genome Medicine 2013, 5:37 (30 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Kuzmanov and Emili review recent advances in protein-protein interaction studies from various model organisms, shedding light on the mechanisms and possible treatments for human disease.
		Musings The Human Genome Organisation: towards next-generation ethics Bartha Knoppers, Adrian Thorogood, Ruth Chadwick Genome Medicine 2013, 5:38 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Knoppers, Thorogood and Chadwick muse over the evolution of ethical statements and policy over the course of the human genome project and beyond, marking 10 years since its completion.
		Review Genomics and outbreak investigation: from sequence to consequence Esther R Robinson, Timothy M Walker, Mark J Pallen Genome Medicine 2013, 5:36 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mark Pallen and co-authors review advances in applying high-throughput sequencing approaches for outbreak investigation (focusing on bacterial infections), and discuss the implications for clinical microbiology.
		Research highlight Plasma-seq: a novel strategy for metastatic prostate cancer analysis Caitlin Farris, Jeffrey M Trimarchi Genome Medicine 2013, 5:35 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Caitlin Farris and Jeffrey Trimarchi discuss how a new non-invasive approach for personalized diagnosis of prostate cancer shows promise for the clinic, being both time- and cost-effective.
		Review The genomics of preterm birth: from animal models to human studies Katherine Y Bezold, Minna K Karjalainen, Mikko Hallman, Kari Teramo, Louis J Muglia Genome Medicine 2013, 5:34 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Louis Muglia and colleagues review the genetics and genomics of pre-term birth and birth timing, discussing the limitations of animal models and the progress of human studies.
		Method Development and validation of a robust automated analysis of plasma phospholipid fatty acids for metabolic phenotyping of large epidemiological studies Laura Wang, Keith Summerhill, Carmen Rodriguez-Canas, Ian Mather, Pinal Patel, Michael Eiden, Stephen Young, Nita G Forouhi, Albert Koulman Genome Medicine 2013, 5:39 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fully automated high-throughput method provides proof-of-concept that fatty acid profiling of human plasma is achievable for metabolic phenotyping in large epidemiological and genetic studies.
		Musings Are randomized trials obsolete or more important than ever in the genomic era? John PA Ioannidis, Muin J Khoury Genome Medicine 2013, 5:32 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary John Ioannidis and Muin Khoury reflect on how advances in the field of genomics are questioning the need for randomized clinical trials and revolutionizing their design.
		Editorial Microbial genomics: an increasingly revealing interface in human health and disease Martin L Hibberd Genome Medicine 2013, 5:31 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Guest Editor Martin Hibberd highlights advances in genomics, metagenomics and other high-throughput approaches for studying human-microbe interactions in health and disease, and the applications for medicine.
		Research Isoform level expression profiles provide better cancer signatures than gene level expression profiles ZhongFa Zhang, Sharmistha Pal, Yingtao Bi, Julia Tchou, Ramana V Davuluri Genome Medicine 2013, 5:33 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Expression profiles at the isoform level perform better than those at the gene level to discriminate between cancer cell lines and non-oncogenic cells, regardless of tissue of origin.
		Research Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing Ellen Heitzer, Peter Ulz, Jelena Belic, Stefan Gutschi, Franz Quehenberger, Katja Fischereder, Theresa Benezeder, Martina Auer, Carina Pischler, Sebastian Mannweiler, Martin Pichler, Florian Eisner, Martin Haeusler, Sabine Riethdorf, Klaus Pantel, Hellmut Samonigg, Gerald Hoefler, Herbert Augustin, Jochen B Geigl, Michael R Speicher Genome Medicine 2013, 5:30 (5 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genomic monitoring of prostate cancer using non-invasive plasma DNA sequencing can be carried out quickly and cheaply using a benchtop high-throughput sequencer.
		Method Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction Gerald Quon, Syed Haider, Amit G Deshwar, Ang Cui, Paul C Boutros, Quaid Morris Genome Medicine 2013, 5:29 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The ISOpure algorithm generates a sample-specific gene expression profile, from which the impact of heterogeneous tumor composition is removed, improving prediction of clinical outcome.
		Review Pancreatic cancer genomics: insights and opportunities for clinical translation Alvin Makohon-Moore, Jacqueline A Brosnan, Christine A Iacobuzio-Donahue Genome Medicine 2013, 5:26 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Christine Iacobuzio-Donahue and colleagues review how genome sequencing is uncovering pathways involved in initiation and progression of pancreatic cancer, and the clinical implications.
		Research Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing Jason O'Rawe, Tao Jiang, Guangqing Sun, Yiyang Wu, Wei Wang, Jingchu Hu, Paul Bodily, Lifeng Tian, Hakon Hakonarson, W Evan Johnson, Zhi Wei, Kai Wang, Gholson J Lyon Genome Medicine 2013, 5:28 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Head-to-head comparison of widely used variant calling pipelines including SOAP, GATK and Complete Genomics using default parameters reveals discrepancies between the pipelines.
		Opinion Harm, hype and evidence: ELSI research and policy guidance Timothy Caulfield, Subhashini Chandrasekharan, Yann Joly, Robert Cook-Deegan Genome Medicine 2013, 5:21 (26 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Timothy Caulfield and colleagues argue that the development of policies for genomic research and medicine will be improved by efforts to incorporate evidence from ELSI research.