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Mapping Bias

A Bioinformatics paper from Jonathan Pritchard's lab at the University of Chicago looked into how SNP variation affects read-mapping reliability, particularly in relation to allele-specific expression. "We have shown here that differential mapping of SNP alleles can greatly affect inferences that rely on quantifying DNA or RNA with next-generation sequencing data. This may be especially problematic in studies that aim to detect allele-specific differences in gene expression, transcription factor binding or other related applications," the authors write.

Dan Koboldt at MassGenomics weighs in on the study. "Your reaction might be to shrug, since Illumina/Solexa now routinely generates 76-bp and 100-bp reads," he says, adding that there are "a number of reasons why this might not address the bias issue" including that the lengths of alignment seeds have not changed and that many groups are still rely on shorter reads.

The Scan

mRNA-Based Vaccine on the Way in China

China may soon have its own mRNA-based vaccine, according to Nature News.

Arranged Killing, Fraud Alleged by Prosecutors

The Wall Street Journal reports that prosecutors allege that the co-founder of a biotech arranged to have a business associate who threatened to expose him as a fraud killed.

Whirlwind Decade of CRISPR

The New York Times looks back at the 10 years since the University of California, Berkeley's Jennifer Doudna and her colleagues published their CRISPR paper.

PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

In PNAS this week: structural variants linked to blue cone monochromacy, HIV-1 variants affecting the matrix protein p17, and more.