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Diagnostic genomics

Guest editors: James Lupski and Joris Veltman

Whole genome and exome sequencing are now being implemented in the clinic. Leading hospitals around the world have undertaken thousands of sequencing tests on patients, and recent reports have demonstrated a diagnostic success rate of around 25%, with higher rates for certain disorders. To mark this important move into the clinic, Genome Medicine is pleased to announce a special issue on Diagnostic Genomics from guest editors Joris Veltman, from Radboud University Medical Centre, and Jim Lupski, from Baylor College of Medicine.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process.

  1. Content type: Database

    The Cancer Genome Atlas (TCGA) project has generated genomic data sets covering over 20 malignancies. These data provide valuable insights into the underlying genetic and genomic basis of cancer. However, expl...

    Authors: HoJoon Lee, Jennifer Palm, Susan M. Grimes and Hanlee P. Ji

    Citation: Genome Medicine 2015 7:112

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  2. Content type: Method

    While the cost of whole genome sequencing (WGS) is approaching the realm of routine medical tests, it remains too tardy to help guide the management of many acute medical conditions. Rapid WGS is imperative in...

    Authors: Neil A. Miller, Emily G. Farrow, Margaret Gibson, Laurel K. Willig, Greyson Twist, Byunggil Yoo, Tyler Marrs, Shane Corder, Lisa Krivohlavek, Adam Walter, Josh E. Petrikin, Carol J. Saunders, Isabelle Thiffault, Sarah E. Soden, Laurie D. Smith, Darrell L. Dinwiddie…

    Citation: Genome Medicine 2015 7:100

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  3. Content type: Method

    We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, ...

    Authors: Alexander L. Greninger, Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M. Linnen, Roger Dodd, Prime Mulembakani, Bradley S. Schneider, Jean-Jacques Muyembe-Tamfum, Susan L. Stramer and Charles Y. Chiu

    Citation: Genome Medicine 2015 7:99

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  4. Content type: Research

    Neurodevelopmental disorders such as autism and intellectual disability have a sex bias skewed towards boys; however, systematic assessment of this bias is complicated by the presence of significant genetic an...

    Authors: Andrew Polyak, Jill A. Rosenfeld and Santhosh Girirajan

    Citation: Genome Medicine 2015 7:94

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  5. Content type: Research

    Personalized medicine is predicated on the notion that individual biochemical and genomic profiles are relatively constant in times of good health and to some extent predictive of disease or therapeutic respon...

    Authors: Rubina Tabassum, Ambily Sivadas, Vartika Agrawal, Haozheng Tian, Dalia Arafat and Greg Gibson

    Citation: Genome Medicine 2015 7:88

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  6. Content type: Opinion

    Incidental findings are the subject of intense ethical debate in medical genomic research. Every human genome contains a number of potentially disease-causing alterations that may be detected during comprehens...

    Authors: Sebastian Schuol, Christoph Schickhardt, Stefan Wiemann, Claus R. Bartram, Klaus Tanner, Roland Eils, Benjamin Meder, Daniela Richter, Hanno Glimm, Christof von Kalle and Eva C. Winkler

    Citation: Genome Medicine 2015 7:83

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  7. Content type: Review

    As a result of multiple technological and practical advances, high-throughput sequencing, known more commonly as “next-generation” sequencing (NGS), can now be incorporated into standard clinical practice. Whe...

    Authors: Jeffrey Gagan and Eliezer M. Van Allen

    Citation: Genome Medicine 2015 7:80

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  8. Content type: Software

    Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGen...

    Authors: Jinlian Wang, Jun Liao, Jinglan Zhang, Wei-Yi Cheng, Jörg Hakenberg, Meng Ma, Bryn D. Webb, Rajasekar Ramasamudram-chakravarthi, Lisa Karger, Lakshmi Mehta, Ruth Kornreich, George A. Diaz, Shuyu Li, Lisa Edelmann and Rong Chen

    Citation: Genome Medicine 2015 7:77

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  9. Content type: Comment

    Expanded genetic carrier testing is changing clinical practice. Current experience highlights the need for rigorous curation of tens of thousands of variants as to their pathogenicity and phenotypic effects. T...

    Authors: Arthur L. Beaudet

    Citation: Genome Medicine 2015 7:79

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  10. Content type: Editorial

    Next-generation sequencing is revolutionizing medical genetics and in the near future will pervade all medical fields. To maximize the potential clinical utility of this approach, global data sharing and pheno...

    Authors: Joris A. Veltman and James R. Lupski

    Citation: Genome Medicine 2015 7:78

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  11. Content type: Method

    Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical d...

    Authors: Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter and Nazneen Rahman

    Citation: Genome Medicine 2015 7:76

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  12. Content type: Method

    Reliable detection of somatic copy-number alterations (sCNAs) in tumors using whole-exome sequencing (WES) remains challenging owing to technical (inherent noise) and sample-associated variability in WES data....

    Authors: Vinay Varadan, Salendra Singh, Arman Nosrati, Lakshmeswari Ravi, James Lutterbaugh, Jill S. Barnholtz-Sloan, Sanford D. Markowitz, Joseph E. Willis and Kishore Guda

    Citation: Genome Medicine 2015 7:69

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  13. Content type: Research

    Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. ...

    Authors: Anil Patwardhan, Jason Harris, Nan Leng, Gabor Bartha, Deanna M. Church, Shujun Luo, Christian Haudenschild, Mark Pratt, Justin Zook, Marc Salit, Jeanie Tirch, Massimo Morra, Stephen Chervitz, Ming Li, Michael Clark, Sarah Garcia…

    Citation: Genome Medicine 2015 7:71

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  14. Content type: Software

    The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical geno...

    Authors: Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, Andrew Lonie, Sebastian Lunke, Ivan Macciocca, Jason P. Ross, Kirby R. Siemering, Zornitza Stark, Susan M. White, Graham Taylor, Clara Gaff, Alicia Oshlack and Natalie P. Thorne

    Citation: Genome Medicine 2015 7:68

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  15. Content type: Research

    In an effort to return actionable results from variant data to electronic health records (EHRs), participants in the Electronic Medical Records and Genomics (eMERGE) Network are being sequenced with the target...

    Authors: David R. Crosslin, Peggy D. Robertson, David S. Carrell, Adam S. Gordon, David S. Hanna, Amber Burt, Stephanie M. Fullerton, Aaron Scrol, James Ralston, Kathleen Leppig, Andrea Hartzler, Eric Baldwin, Mariza de Andrade, Iftikhar J. Kullo, Gerard Tromp, Kimberly F. Doheny…

    Citation: Genome Medicine 2015 7:67

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  16. Content type: Research

    Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases wh...

    Authors: Chulin Sha, Sharon Barrans, Matthew A. Care, David Cunningham, Reuben M. Tooze, Andrew Jack and David R. Westhead

    Citation: Genome Medicine 2015 7:64

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  17. Content type: Research

    High-throughput genetic testing is increasingly applied in clinics. Next-Generation Sequencing (NGS) data analysis however still remains a great challenge. The interpretation of pathogenicity of single variant...

    Authors: Sabine C. Mueller, Christina Backes, Olga V. Kalinina, Benjamin Meder, Daniel Stöckel, Hans-Peter Lenhof, Eckart Meese and Andreas Keller

    Citation: Genome Medicine 2015 7:65

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  18. Content type: Research

    Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potentia...

    Authors: Tomasz Gambin, Shalini N. Jhangiani, Jennifer E. Below, Ian M. Campbell, Wojciech Wiszniewski, Donna M. Muzny, Jeffrey Staples, Alanna C. Morrison, Matthew N. Bainbridge, Samantha Penney, Amy L. McGuire, Richard A. Gibbs, James R. Lupski and Eric Boerwinkle

    Citation: Genome Medicine 2015 7:54

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