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What the Papers Say


Transplant Health
Snyder TM, Khush KK, Valantine HA, et al. (2011). Universal noninvasive detection of solid organ transplant rejection. PNAS. Epub: doi 11073/pnas.1013924108.

Investigators at Stanford University show that shotgun sequencing of cell-free DNA circulating in the blood of organ transplant recipients can be used to detect an organ-specific signature that correlates with rejection. By analyzing cell-free DNA derived from heart transplant recipients' blood, the team "observed significantly increased levels of cell-free DNA from the donor genome" in instances of acute cellular rejection, which was independently established through a standard endomyocardial biopsy. While the authors say that this sequencing-based test "holds promise for replacing the endomyocardial biopsy in heart transplant recipients," they add that it may also be applicable to other solid organ transplants.

Multiple Myeloma Genome
Chapman MA, Lawrence MS, Keats JJ, et al. (2011). Initial genome sequencing and analysis of multiple myeloma. Nature. (471): 467-472.

Broad Institute researchers report on a study of multiple myeloma patients in which they sequenced the whole genomes of 23 patients and sequenced the whole exomes of 16 patients. By comparing tumor versus normal genomes, the team identified a pattern of somatic mutations that suggests "new and unexpected oncogenic mechanisms." As the researchers found activating mutations of BRAF in 4 percent of the patients, they say that BRAF inhibitors should be evaluated in multiple myeloma clinical trials. However, the team also notes that its analysis is preliminary; more sequences will be required to "establish the definitive genomic landscape of the disease and determine accurate estimates of mutation frequency in the disease," the authors write.

A New Osteosarcoma Target
Lockwood WW, Stack D, Morris T, et al. (2011). Cyclin E1 is amplified and overexpressed in osteosarcoma The Journal of Molecular Diagnostics. Epub: doi 10.1016/j.jmoldx.2010.11.020.

Using a whole-genome tiling path array to evaluate copy number changes in 22 osteosarcoma tumor samples, researchers at Our Lady's Children's Hospital, Crumlin, in Dublin and their colleagues validated gains and losses at recognized disease genes of interest and also identified novel targets, including cyclin E1. By performing fluorescence in situ hybridization and immunohistochemical analyses, the team confirmed the involvement of cyclin E1 over-expression in osteosarcoma, a finding it says confers "potential prognostic and therapeutic implications" for the disease.

Sea Bass Map
Wang CM, Baj ZY, He XP, et al. (2011). A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. BMC Genomics. (12): 174.

Gen Hua Yue and his team at the National University of Singapore developed a second-generation linkage map of the Asian sea bass, which allowed them to compare it to the pufferfish Tetraodon nigroviridis genome. Between the two, the team found 16 regions of synteny. Using its linkage map, the Yue group also identified potential candidate genes for growth traits in quantitative trait loci regions. "Interestingly, a QTL cluster at Lca371 underlying growth traits of Asian sea bass showed similarity to the cathepsin D gene of human, which is related to cancer and Alzheimer's disease," the team writes.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.