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Bioinformatician: Down with 'Data Drop'

At his blog, New York University's Stuart Brown says researchers should speak with their colleagues in bioinformatics before they begin sequencing projects rather than simply dropping off hordes of fresh data. Brown says "our informatics effort is much greater on the poorly designed and failed experiments." For example, his department recently processed a "seemingly standard SNP detection using exome sequences with 100 [base pair] paired-end reads … done by a private sequencing contractor" that'd also called some SNPs. In searching for overlaps between SNP calls for a variety of samples and controls, Brown and his bioinformatics colleagues found that the sequencing reads generated by the contractor "have a 1.5 percent error rate." Given additional quality control data, Brown's group saw "a steep increase in error at the ends of reads," he says. Now, rather than simply searching for overlaps, the bioinformaticians must "trim all reads down by 10 [percent] to 25 percent and recall SNPs." Brown says his group is left to wonder about the sequencing library's insert sizes, and how they may have contributed to the overall error rate. "Talk to bioinformatics before you build your sequencing libraries," Brown pleads.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.