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Justin Petrone is the editor of GenomeWeb's BioArray News and covers the microarray and biochip sector of the genomics market. E-mail Justin Petrone or follow his GenomeWeb Twitter account at @BioArrayNews.
PicoPLEX DNA-Seq: Single Cell Sequencing, Theory and Applications
In this archived webinar, recorded Feb. 19, 2014, two speakers outline applications of Rubicon Genomics' PicoPLEX DNA-seq single cell library preparation kit. Jeramiah Smith, assistant professor of biology at the University of Kentucky, discusses the use of PicoPLEX DNA-seq for de novo sequencing of single amphibian chromosomes, while John Langmore, co-founder and chief scientific officer of Rubicon, details the use of PicoPLEX DNA-seq for aneuploidy, CNV, and STR testing of single human cancer and reproductive cells.
Speakers: Jeramiah Smith, Assistant Professor of Biology, University of Kentucky; and John Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics
Sponsor: Rubicon Genomics
Recording Date: 2/19/2014
Recording Time: 1 hour
Young Investigator Profile
Karolinska Institute, Science for Life Laboratory
Method for Single-cell Resolved Transcriptomics
Patrik Ståhl is a methods developer from way back. His PhD work focused on general genomics and he's ridden the wave over into transcriptomics. Currently, he and his colleagues are working on a spatially resolved transcriptomics method that he said allows single-cell resolution.
Typically transcriptomic analysis is an analysis of an average: A tissue is ground up and its RNA extracted. That RNA gives an overall view of what's going on in that tissue.
Instead, Ståhl's approach relies on overlaying tissue on a microarray surface that is embedded with a number of barcoded features that tell the researchers just where in the tissue a transcript is present.
"It's a totally new method and basically we can get a single-cell resolution in that way, and we can analyze tens of thousands of samples in the same experiment at that resolution," Ståhl said, noting that he and his colleagues are in the process of publishing this work. "Obviously, we are very excited [and] we think that this could really be a huge hit."
In PNAS this week: advantage of pygmy phenotype, optogenetic approach to activate neurons, and more.
Papers of Note
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation Lou, Lee, et al. Genome Biology
An international group led by investigators in Hong Kong used a combination of RNA sequencing, whole-genome bisulfite sequencing, and chromatin immunoprecipitation sequencing to quantify expression, methylation, and histone modification patterns in samples and cell lines from members of a Chinese parent-child trio affected by type 2 diabetes. Generally speaking, the researchers found that high levels of DNA methylation in the promoter region a gene correspond with lower-than-usual expression of the gene. But methylation across the gene body appeared to have a similar effect, prompting the study's authors to argue that "[f]uture studies on gene regulatory mechanisms and disease-associated differential methylation should pay more attention to DNA methylation at gene bodies and other non-promoter regions."
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: An evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina) Schwartze, Winter, et al. PLOS Genetics
The mucormycosis infection-causing fungal pathogen Lichtheimia corymbifera appears to have undergone gene duplications and genome expansions in the absence of duplications affecting the whole genome. A team from Germany, Spain, and Brazil used a combination of Roche 454 and Illumina approaches to sequence the L. corymbifera genome before comparing it to sequences from another fungal pathogen that can cause mucormycosis, called Rhizopus oryzae. The comparison indicated that the L. corymbifera genome contains a slew of duplicated genes that have taken on diverse functions, for example, but a relative lack of repeat sequences and alternative splicing.
People on the Move
The New York Genome Center has named Carol Ashe its new chief business officer. She previously served as VP of corporate development for pharmaceutical firm Endo International, and prior to that was a partner at GlaxoSmithKline's venture capital fund, SR One. Ashe also led GSK's US corporate legal group, which supported M&A transactions and the business development legal transactions team.
Vermillion has named David Jansen its VP of marketing, a new position at the firm. Jansen joins Vermillion from Myriad Genetics, where he held senior marketing roles for the past seven years. Vermillion also said that Chief Commercial Officer Marian Sacco will be leaving the company as part of a reorganization and restructuring. Sacco had joined the firm just last December.
Epic Sciences has appointed Greg Lucier as chairman of its board of directors. Lucier was previously chairman and CEO of Life Technologies.
Illumina said this week it has appointed Google Senior Vice President Jeff Huber to serve on its board of directors. Huber, who works with the Google X research branch, joined Google in 2003 and led development of Google Maps, Google Apps, and Google Ads. He also formerly was VP of architecture and systems development at eBay, and senior VP of engineering at Excite@Home.
Conferences, Meetings & Deadlines
MSACL 2014 EU
September 2-5 / Salzburg, Austria
The Association for Mass Spectrometry Applications to the Clinical Lab
Using the CRISPR/Cas9 genome editing system, researchers from the University of Texas Southwestern Medical Center were able to prevent Duchenne muscular dystrophy in a mouse model of the disease. The researchers aimed to correct the nonsense mutation in exon 23 of the Dmd gene that the mdx mouse model of Duchenne muscle dystrophy harbors. Sequencing of the mice revealed that CRISPR/Cas9–mediated germline editing led to genetically mosaic corrected mice, which had between 2 percent and 100 percent correction of the Dmd gene.
The FDA has approved Exact Sciences' Cologuard colorectal cancer screening test, while the CMS issued a proposed national coverage determination for the test. The test analyzes hemoglobin, multiple DNA methylation biomarkers, mutations in the KRAS gene, and the total amount of DNA in stool samples. CMS is proposing to cover testing using Cologuard once every three years for Medicare beneficiaries who are between the ages of 50 and 85, are asymptomatic for colorectal disease, and are at average risk for developing the disease.
The National Institute of General Medical Sciences will provide up to $2 million per year to renew funding for each of the National Centers for Systems Biology, pending approval of renewal applications. NIGMS currently funds 12 systems biology centers at institutions across the US that use a wide range of molecular, cellular, biochemical, behavioral, and other approaches to study complex biological phenomena. The systems biology centers program is currently under evaluation, NIGMS said, so it is not currently offering awards to fund new centers.
This online seminar will provide an overview of new tools for screening stem cells — in particular, the use of RNA detection probes to detect pluripotency gene expression in live embryonic and induced pluripotent stem cells by fluorescence microscopy without the need for manipulation of the cells.