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Genomics in the Journals: Feb 17, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Members of the 1000 Genomes Project revisited population-level structural variation in the human genome by using an analytical approach to track down and characterize deletion polymorphisms in 168 human genomes. The team genotyped nearly 14,000 deletion polymorphisms in the genomes, which had been sequenced to an average of four times coverage for the pilot phase of the international project — work that they outlined online in Nature Genetics this week.

"We have described a new analytical framework for analyzing sequence data that arise from a large number of genomes," senior author Steven McCarroll, a researcher at Harvard Medical School and the Broad Institute, and co-authors wrote. "Together with methods for analyzing single-nucleotide variation and small indels, these approaches will help realize the scientific potential of sequence data that are generated at a population scale."


In an online mBio paper, a pair of researchers from Northwestern University reported that they detected bits of human DNA in publicly available Neisseria gonorrhoeae genome sequences. The duo found evidence of horizontal gene transfer involving a human long interspersed nuclear element known as L1 in about 11 percent of N. gonorrhoeae genomes assessed. L1 transcripts also turned up in the duo's reverse transcription PCR experiments, suggesting the human sequence can be expressed by the gonorrhea-causing bug.


Hundreds of non-primate DNA sequences found in public databases are contaminated with human DNA sequences, University of Connecticut researchers reported in PLoS ONE. The team found that 492 of the 2,749 non-primate sequences screened in NCBI, JGI, UCSC, and Ensembl databases contained AluY short interspersed nucleotide element sequences that are primate specific.

"The level of contamination found in these databases is significant and worrisome," senior author Rachel O'Neill, a molecular and cell biology researcher at UConn, and her co-authors said, arguing that their work "points to a need for more rigorous pre-sequencing protocols and laboratory standards."


In a Science Policy Forum article, a team of genetics and bioethics researchers from the University of North Carolina at Chapel Hill, Indiana University, King's College London, and the University of Alberta discuss what they call the 'genomic bubble," arguing that researchers and funding agencies should not lose site of larger goals — such as better human health — in their zeal for genomics.

"If we fail to evaluate the considerable promise of genomics through a realistic lens, exaggerated expectations will undermine its legitimacy, threaten its sustainability, and result in misallocation of resources," they write. "Fueling unrealistic expectations for predictive genetic testing and uncritical translation of discoveries may also distract our gaze from other promising approaches to preventing disease and improving health."


Meanwhile, in its third week of perspectives articles on human genomics, Science features pieces by Harvard University science and technology researcher Sheila Jasanoff; University of Washington researcher Maynard Olson; Shinya Yamanaka, director of Kyoto University's Center for iPS Cell Research and Application; United Arab Emirates University genetics and pediatrics researcher Lihadh Al-Gazali; Robert Cook-Deegan, director of Duke University's Institute for Genome Sciences and Policy; University of Queensland researcher John Mattick; and University of Stellenbosch researcher Eileen Hoal.


Genomics In The Journals is a new weekly feature pointing readers to select, recently published articles involving genomics and related research.

The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.