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A New Approach to Finding Copy Number Aberrations

An advance article in Bioinformatics discusses a new approach, called Correlation Matrix Diagonal Segmentation, that identifies recurrent DNA copy number aberration using a between-chromosomal-site correlation analysis. At MassGenomics, Dan Koboldt, a co-worker of the authors, describes how they evaluated the tool with lung adenocarcinoma and glioblastoma datasets from the Tumor Sequencing Project and the Cancer Genome Atlas. The researchers were able to call 39 recurrent copy number aberration regions in lung cancer and 37 in brain cancer — all of which had previously reported. Kobolt adds that the Correlation Matrix Diagonal Segmentation is fast: “The R version of CMDS finished in 13 seconds. The other algorithms took more than 300 times longer on the same dataset, indicating that CMDS represents a substantial performance gain. There’s also a C version of CMDS that runs even faster.”

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

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.