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Nature Papers Describe Benchmarks for Challenging Genes, Approach to Detect Unamplified Nucleic Acids

Highly curated benchmarks for nearly 300 medically relevant and challenging genes not included in the Genome in a Bottle Consortium's (GIAB) benchmark sets are reported in Nature Biotechnology this week. The GIAB develops benchmarks to advance accurate human genomic research and clinical applications of sequencing, but multiple regions of the genome remain unresolved by the consortium due to repetitive sequences, segmental duplications, and complex variants. In a new paper, a Baylor College of Medicine-led team characterizes 273 challenging autosomal genes missing from the GIAB's benchmarks using a haplotype-resolved whole-genome assembly. "This benchmark enables a more comprehensive assessment of sequencing strategies, analytical methodologies, and other developments for challenging genomic variants and regions relevant to medical research, paving the way for improved clinical diagnoses," they write.

A novel method for the rapid and ultrasensitive detection of unamplified nucleic acids in biofluids is presented in this week's Nature Biomedical Engineering. Many disease-relevant biomarkers are present at very low abundances in biofluids, and it remains technically challenging to detect them through orders-of-magnitude higher amounts of background biomolecules. To address this, a group led by researchers from Fudan University developed a molecular system — immobilized on a liquid-gated graphene field-effect transistor and consisting of an aptamer probe bound to a flexible single-stranded DNA cantilever linked to a self-assembled stiff tetrahedral double-stranded DNA structure — for the electromechanical detection of unamplified nucleic acid, ions, small molecules, and proteins at levels as low as one to two copies in 100 μl of biofluid. They demonstrate the technology by integrating it into a portable device that can detect SARS-CoV-2 RNA in less than four minutes in nasopharyngeal samples without the need for RNA extraction or nucleic acid amplification.

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