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This Week in Genome Research: Dec 23, 2009

In Genome Research this week, European researchers used bead arrays and bisulfite sequencing to find methylation changes linked to systemic lupus erythrematosus in pairs of identical twins who were discordant for the autoimmune disease — especially at genes involved in immune function. Their follow-up experiments suggest those with lupus tend to have lower levels of 5-methylcytosine, less methylation at certain genes, and higher expression of these genes. "Our findings not only identify potentially relevant DNA methylation markers for the clinical characterization of SLE patients but also support the notion that epigenetic changes may be critical in the clinical manifestations of autoimmune disease," the researchers write. A related news story on our sister publication GenomeWeb Daily News has more details.

Meanwhile, a group of researchers from the Baylor College of Medicine, Rice University, and Washington University report that they have come up with a way to sift through large amounts of high-throughput re-sequencing data and pick out genetic variants without getting duped by sequencing errors. Their computational tool — called Atlas-SNP2 — takes into account sequence context in training datasets to help distinguish between errors and authentic SNPs with a less than 10 percent false-positive error rate and a false-negative error rate of five percent or so.

In a companion article to their recent Nature Biotechnology paper on tackling a human pan-genome, scientists from the Beijing Genomics Institute at Shenzhen and University of Copenhagen reported on their method for assembling African and Asian human genomes from short read sequences using the SOAPdenovo algorithm. "The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way," the team writes.

Finally, investigators from the University of Chicago and Yale University used RNA sequencing to explore sex- and lineage-specific alternative splicing in primates. Their work on humans, chimps, and rhesus macaques indicates that "while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent." They also found hints that differences in alternative splicing regulation may have had a hand in human evolution.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.