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This Week in Genome Research: Apr 24, 2019

Researchers from the University of California, San Francisco, and elsewhere present a validated clinical assay for detecting pathogens by metagenomic sequencing on cerebrospinal fluid samples. The team applied the approach — which includes a custom bioinformatics pipeline called SURPI+ — to CSF samples from individuals with meningitis or encephalitis. In blind testing on CSF samples from 95 patients, the authors report, the metagenomic next-generation sequencing assay picked up the pathogen culprits with 73 percent sensitivity and 99 percent specificity relative to prior clinical test results. And in samples from 20 children with meningitis, encephalitis, or myelitis, they saw a sensitivity of 92 percent and 96 percent specificity compared with results from standard microbial tests on CSF samples. 

A BGI-Shenzhen- and Complete Genomics-led team outlines a "single-tube long fragment read" (stLFR) approach for doing affordable sequencing, haplotyping, and de novo assembly with co-barcoded second-generation sequencing reads. For the co-barcoding step, the researchers say, they use surface microbeads to incorporate the same barcode sequence across sub-fragments from the same long DNA molecules in one sample prep tube. After showing that they could add distinct barcodes to more than eight million fragments running 20,000 to 300,000 bases apiece, they went on to use stLFR for assessing structural variants, phase blocks, and other features in single libraries of the NA12878 human genome.

Finally, researchers at UCSF and elsewhere explore ancestry, admixture, and more with high-coverage whole-genome sequences for 100 captive baboons from a pedigreed colony at the Southwest National Primate Research Center that includes olive (Papio anubis) and yellow (P. cynocephalus) baboon species. The team generated between 21- and 42-fold average coverage of the baboon genomes, aligning the sequences to an available reference genome to get a look fine-map recombination rates. The baboon genome sequence also made it possible to start digging into common variant patterns in the baboons, and comparing ancestry and other features in the olive and yellow baboon species. For example, the authors note, the sequences highlight deleterious variants passed on by inbreeding that may increase infant mortality.