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This Week in PNAS: Dec 4, 2018

Researchers from Kyoto University and elsewhere report on genetic contributors to the systemic blood vessel inflammation condition Takayasu arteritis (TAK), identified with a genome-wide association study, functional annotation, and pathway-based analyses. Based on data for 633 individuals with TAK and more than 5,900 unaffected control individuals, the team tracked down four new risk loci with significant ties to TAK, while fine-mapping a known susceptibility locus at the human leukocyte antigen locus HLA-B*52 and fleshing out a role for the immune system's natural killer cells in TAK with enhancer enrichment analyses. "Not only the associations in the HLA region but also non-significant associations from GWAS suggest the involvement of [natural killer] cells," the authors write.

An international team led by investigators in China describes more than a dozen expression-based subgroups for B-cell precursor acute lymphoblastic leukemia. Using RNA sequencing, the researchers looked at the transcriptional landscape in 1,223 BCP ALL cases, providing an improved look at eight known expression subgroups and six subgroups not described in the childhood blood cancer previously. At least some of the new subgroups — marked by specific gene fusions or mutations — seem to provide clues to BCP ALL classification and prognosis, the authors report, noting that "RNA sequencing should be a valuable tool in the routine diagnostic workup for ALL."

University of Alabama at Birmingham researchers explore DNA template sequence effects on RNA polymerase I (Pol I) transcription elongation kinetics in vitro and in vivo. After looking at the ways that Pol I activity was altered in Saccharomyces cerevisiae containing an Escherichia coli terminator motif, the team used native elongating transcript sequencing to find ribosomal DNA positions that prompted Pol I pausing in response in the S. cerevisiae budding yeast in vivo. "These data demonstrate that DNA template sequence elements directly influence Pol I transcription elongation," the investigators report, adding that "we have developed the necessary experimental and analytical methods to investigate these perturbations in living cells going forward."

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.