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
University of Washington
Increasing What Sequencing Can Do
There's a lot that sequencing can do, but there are still plenty of things that it cannot do. Jacob Kitzman's work on sequencing technology in general, and on haplotype sequencing in particular, sprung in part from the desire to chip away at what sequencing can't do.
"We were motivated [by] interesting areas of biology that demanded essentially better sequencing, better continuity," Kitzman said. Indeed, better haplotype sequencing has enabled both prenatal and cancer genomic studies.
Kitzman will be starting his own lab this spring at the University of Michigan, where he plans to branch out a little bit, though he'll continue to work on developing new sequencing technologies.
He said that he and his team would focus on studying somatic variations and genetic diversity. In particular, he said he plans to focus on how to sequence difficult, diverse areas like the HLA locus, using either technology developed in house or elsewhere.
A genome sequencing study by researchers from Massachusetts provides a peek at the processes behind small-cell lung carcinoma development and progression. The team developed a genetically engineered mouse model of the small-cell lung carcinoma missing two of the genes that have previously been shown to be oft-mutated in human forms of the disease. By sequencing the genomes or exomes of primary or metastatic tumors that developed in six of the mice, together with matched normal tissue sample, the investigators narrowed in on recurrent copy number changes, rearrangements, and somatic mutations in the mouse models of small-cell lung carcinoma. They also tracked down patterns associated with metastasis, including sequential alterations in tumors that spread to other parts of the body.
A Peking University-led team describes RNA editing patterns they detected by sequencing DNA and RNA from multiple rhesus macaque tissues. Using data from one rhesus macaque, the researchers narrowed in on some 31,250 examples of RNA editing. Most of those appeared to be adenine to guanine swaps, they note, apparently due to adenosine deamination. "[T]he macaque editome reported here highlights RNA editing as a widespread functional regulation in primate evolution," they conclude, "and provides an informative framework for further understanding RNA editing in human."
People on the Move
CollabRx has appointed Paul Billings to its board of directors. Billings is a board certified internist and clinical geneticist and most recently served as chief medical officer for Life Technologies. He is executive chairman of Melanoma Diagnostics, a director of Trovagene, and a co-founder and past medical director of the Cordblood Registry. He was also a senior vice president for corporate development at Laboratory Corporation of America and a co-founder of Omicia. Billings also currently serves on the Scientific Advisory Board of the US Food and Drug Administration, the Genomic Medicine Advisory Committee at the Department of Veterans Affairs, and the National Academy of Sciences Institute of Medicine’s Roundtable on Genomics.
Kathy Hibbs, former senior VP and general counsel at Genomic Health, has joined 23andMe as chief legal and regulatory officer. Hibbs joins 23andMe while the firm is in the midst of regulatory discussions with the US Food and Drug Administration regarding its Personal Genome Service. Hibbs has also worked at Monogram Biosciences and Varian Medical Systems, and is actively engaged in a number of industry groups, such as the American Clinical Laboratory Association, the Coalition for 21st Century Medicine, and the Personalized Medicine Coalition.
Stephen Rusckowski has been named chairman of the American Clinical Laboratory Association's board of directors. Rusckowski has served as Quest Diagnostics' president and CEO since May 2012. Before joining Quest Diagnostics he was CEO of Philips Healthcare.
ProteinSimple has appointed Joe Keegan and Chris van Ingen to its board of directors. Keegan was previously the CEO of ForteBio and Molecular Devices. Van Ingen was previously president of Agilent Technologies' bio-analytical measurement business. He currently serves on the boards of Bruker, Accelrys, and Promega.
An international team of investigators in the UK, Turkey, and elsewhere sequenced the genomes of nearly 100 MRSA isolates — a collection that showed widely variable toxicity profiles in their cell- and mouse-based assays. The team's analysis led to a genetic signature that appeared to coincide with the most pronounced toxicity patterns in the MRSA isolates. Those snippets of sequence subsequently proved useful for predicting which isolates would have high or low toxicity in a mouse model of MRSA infection.
Myriad Genetics has submitted to the US Food and Drug Administration the first module of its premarket approval application for BRACAnalysis as a companion test for AstraZeneca's breast cancer PARP inhibitor olaparib. The test is being used in two Phase III trials to pick out ovarian cancer patients who harbor BRCA mutations and as such are thought to be best responders to olaparib. Myriad filed an investigational device exemption application with the FDA less than a year ago to enable it to use BRACAnalysis in these studies.
A research team at Washington University School of Medicine in St. Louis plans to use an $8 million grant from the National Heart, Lung, and Blood Institute to conduct a large-scale analysis of genetic and lifestyle data from multi-ethnic cohorts. The scientists plan to examine data from more than 30 studies, including genomic information, common cardiovascular measures, and a range of lifestyle factors, to try to identify interactions between genetics and lifestyle that impact cardiovascular disease risk.
GenomeWeb and Myriad RBM invite you to a free online presentation by Matthew Albert of the Institut Pasteur on recent progress in personalized immune response monitoring.
Dr. Albert will share findings from the Milieu Interieur Project, a population-based study that aims to identify the genetic and environmental determinants of immune phenotype variance and establish a path towards personalized medicine.