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Journal Club


Dog Diversity
Boyko AR, Quignon P, Li L, et al. (2010). A simple genetic architecture underlies morphological variation in dogs. PLoS Biology. 8(8): e1000451.

Adam Boyko at the Stanford School of Medicine and his colleagues at the National Human Genome -Research Institute and elsewhere have identified 51 regions of the canine genome associated with variation among breeds in their genotyping investigation of 915 dogs. They found a small number of quantitative trait loci that explain the majority of phenotypic variation for the 57 traits they examined, and report that many regions of the dog genome show signatures of recent selection. "The remarkable diversity of form in the dog, in contrast to some other species studied to date, appears to have a simple genetic basis dominated by genes of major effect," Boyko et al. write.

Kabuki Cause
Ng SB, Bigham AW, Buckingham KJ, et al. (2010). Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genetics. doi:10.1038.

By sequencing the exomes of 10 unrelated individuals, the University of Washington's Jay Shendure and his colleagues identified mutations in MLL2, which they suggest "are a major cause of Kabuki syndrome." Shendure et al. found mutations of MLL2, which encodes a trithorax-group histone methyltransferase and contributes to developmental processes, in seven of the 10 probands. Using Sanger sequencing, the team subsequently found MLL2 mutations in two of the remaining three individuals. "In families where parental DNA was available, the mutation was confirmed to be de novo," the authors add.

Nano(porin) Sequencing
Derrington IM, Butler TZ, Collins MD, et al. (2010). Nanopore DNA sequencing with MspA. PNAS. doi/10.1073/pnas.1001831107.

Ian Derrington and his colleagues at the University of Washington report on a proof-of-principle study of their nanopore DNA sequencing method using Mycobacterium smegmatis porin A. "The ionic current through the engineered ... MspA has the ability to distinguish all four DNA nucleotides and resolve single nucleotides in single-stranded DNA when double-stranded DNA temporarily holds the nucleotides in the pore constriction," the authors write. The researchers describe what they call duplex interrupted sequencing, which they suggest allows for less-demanding DNA conversion "because each inserted DNA could be identical and independent of the analyte nucleotides."

Precise Primers
Adomas AB, Lopez-Giraldez F, Clark TA, et al. (2010). Multi-targeted priming for genome-wide gene expression assays. BMC Genomics. (11):477.

Aleksandra Adomas and her colleagues used a novel algorithm to distinguish two multi-targeted primers that "prime a preponderance of genes in the genomes of Saccharomyces cerevisiae and Neurospora crassa while avoiding priming ribosomal RNA or transfer RNA." In assessing the accuracy of their primer sets, the team found that "priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression." The authors suggest that, as a result of the primers, their study presents the "most complete and detailed expression profiles of the yeast nitrogen starvation response and N. crassa early sexual development to date."

The Scan

Response Too Slow, Cautious

A new report criticizes the global response to the threat of the COVID-19 pandemic, Nature News reports.

Pushed a Bit Later

Novavax has pushed back its timeline for filing for authorization for its SARS-CoV-2 vaccine, according to Bloomberg.

AMA Announces Anti-Racism Effort

The Associated Press reports that the American Medical Association has released a plan to address systemic racism in healthcare.

Nucleic Acids Research Papers on miRMaster 2.0, MutationTaster2021, LipidSuite

In Nucleic Acids Research this week: tool to examine small non-coding RNAs, approach to predict ramifications of DNA variants, and more.