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Centralizing Clinical Variants

The National Center for Biotechnology Information's ClinVar database is proving useful for clinical labs trying to interpret genetic variants uncovered by next-gen sequencing, reports Nature.

ClinVar, designed to house information on the relationships between human variations and phenotypes, not only integrates clinical variation data from numerous publicly available resources, but "also provides, for the first time, a central place in which clinical testing laboratories can deposit their data," Nature says.

Clinical sequencing labs have to perform a considerable amount of analysis on novel variants to determine whether they are benign or pathogenic. But keeping this data in house means that many groups are duplicating their efforts.

"There is a growing recognition that a clinical lab may see a mutation once or never, so it’s better if all those data could be pooled,” says James Ostell, chief of the information engineering branch at NCBI.

“For everybody in the field, I think there will be a sigh of relief that this is finally happening,” adds Stephen Kingsmore of the Children’s Mercy Center for Pediatric Genome Medicine.

He says that when clinical labs share their data through ClinVar, “patients are going to be getting the best thinking of the community as opposed to an individual lab.”

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.