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Downloads & Upgrades: Exemplar Dx LIMS; caBIG Community Code Resource Directory; UCSC Genes track

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This week, Sapio Sciences released Exemplar Dx LIMS, a version of its laboratory information management system designed specifically for the molecular diagnostic market.

The product includes features such as an ordering system for physicians to enter test requests; collection kit management; pathology lab interfaces; sample management/lab workflow tracking; instrument integrations for lab automation; assay data management; and custom algorithm implementation among other capabilities.


The National Cancer Institute's Center for Biomedical Informatics and Information Technology has launched the caBIG Community Code Resource Directory, a resource intended to promote the exchange of community-developed digital capabilities supporting cancer research.

The directory provides access to resources developed in support of local informatics needs that may also be of value to the broader cancer research community.


The genome browser team at the University of California, Santa Cruz, has released an updated UCSC Genes track for the GRCh37/hg19 human genome browser.

The release includes more noncoding transcripts based on data from Rfam and the tRNA Genes track at UCSC. It also includes improvements to the UCSC Genes build pipeline such as new genomic alignment protocols for aligning short sequences, a bug fix, and the addition of two new tables that contain sequence data derived from the genome rather than from the mRNA used for the transcript, among other updates.

The release has 80,922 total transcripts, compared with 77,614 in the previous version, and the total number of canonical genes has increased to 31,227 from 27,297.


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.