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Monday, January 29, 2018

Small Creature, Massive Genome: Axolotl Offers Insights Into Regeneration

The Mexican salamander, or the axolotl, may have tiny feet, but the feat of decoding its genetic footprint was huge—32 billion base pairs huge, making it ten times bigger than the human genome and the largest ever sequenced. The accomplishment by an international team of scientists is significant, not only because of its sheer size, but also because of the insights it could provide into tissue regeneration. The easily recognizable critter has an astounding ability to regenerate body parts, growing lost limbs – bones, muscles, nerves and all – within weeks. It can also repair spinal cord and retinal tissue,…

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Wednesday, January 17, 2018

SOLVE-RD Funded to Improve Diagnosis of Rare Disease with New Tools Including Long-Read Sequencing

The SOLVE-RD research program, a collaboration of 21 participant organizations in 10 nations, announced it has received a €15 million grant from the European Union’s Horizon 2020 initiative. SOLVE-RD aims to improve the diagnosis and treatment of rare diseases, which in total affect millions of Europeans. The program is applying novel diagnostic tools to around 19,000 cases unsolved by prior short-read exome sequencing. Prominent among the planned “multi-omics” approach is long-read genome sequencing, which will reveal the large amount of potentially disease-causing genetic variation that is not accessible with short-read DNA sequencing. SOLVE-RD plans to apply long-read genome sequencing to 500…

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Monday, January 15, 2018

When A Single Reference is Not Enough

Maize is amazingly diverse. A study comparing genome segments from two inbred lines, for instance, revealed that half of the sequence and one-third of the gene content was not shared – that’s more diversity within the species than between some other species, for example humans and chimpanzees, which exhibit more than 98 percent sequence similarity. So how can researchers and commercial breeders rely upon a single reference genome to represent the genetic diversity in their germplasms? More and more scientists are deciding they cannot. At DuPont Pioneer, where DNA sequencing is paramount for R&D to reveal the genetic basis for…

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Tuesday, January 9, 2018

Carnivorous Plant Relies on Tandem Duplications for Adaptation

Photo by Kevin Thiele Scientists from the University at Buffalo, Nanyang Technological University, and other institutions published results from an effort to elucidate the Utricularia gibba genome using SMRT Sequencing. U. gibba, also known as the humped bladderwort, is an aquatic carnivorous flowering plant with a remarkably small genome, especially in light of two whole genome duplication events. Genome sequencing and annotation data are reported in the PNAS publication “Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome” from lead author Tianying Lan, senior author Victor Albert, and collaborators. The scientists were interested in using the plant’s genome…

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Friday, January 5, 2018

PMWC 2018: Sequencing Improvements Power Large-Scale Studies and Clinical Assays

One of our favorite January traditions is taking part in the Precision Medicine World Conference (PMWC), a three-day Silicon Valley event focused on exploring challenges and opportunities in personalized medicine. Taking place this year January 22-24 at the Computer History Museum, the slate of more than 350 speakers in 65-plus sessions will offer a cutting-edge look at the field. The conference is co-hosted by Stanford Health Care; the University of California, San Francisco; Johns Hopkins University; the University of Michigan; Duke University; and Duke Health. On the docket this year: PMWC will cover topics including artificial intelligence and machine learning,…

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Thursday, January 4, 2018

Collaborative Effort Results in High-Quality Mosquito Genome, Raising Hope for Infectious Disease Control

In an unprecedented crowd-sourced effort stoked by social media, 72 scientists collaborated via 25 conference calls and 3,323 emails to produce a new high-quality Aedes aegypti mosquito genome. Assembled using PacBio long-read sequencing, the resource could provide the DNA map researchers need to combat the pest and the infectious diseases it spreads, including Zika, dengue, chikungunya, and yellow fever. Eager to share the results with the scientific community, lead author Leslie B. Vosshall, first author Benjamin Matthews, both of Rockefeller University, and colleagues at several other institutions, published a pre-print of their paper, “Improved Aedes aegypti mosquito reference genome assembly…

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Wednesday, January 3, 2018

Alternative Splicing Analysis Reveals Isoforms Associated with FMR1 Repeat Expansion

In a recent publication, scientists from the University of California, Davis, and PacBio reported results from an investigation of alternative splicing associated with a repeat expansion in the gene linked to fragile X syndrome. They used SMRT Sequencing to detect full-length isoforms (Iso-Seq analysis) associated with individuals at risk of FXTAS, an adult-onset neurodegenerative disorder. “Altered expression of the FMR1 splicing variants landscape in premutation carriers” comes from lead author Elizabeth Tseng, senior author Flora Tassone, and collaborators. Previous studies from the Tassone lab had used SMRT Sequencing to detect full-length isoforms in samples from premutation carriers (individuals with more…

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