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 Chicago
Different Approach for Cancer Therapeutics
Tanguy Seiwert knew that he wanted to be able to contribute something to society, and when he was searching for a specialty during his medical training, he thought that the two areas with the highest need were neuroscience and oncology. Cancer, though, seemed to Seiwert to be a more interesting problem, and it also touched home as his grandfather died from cancer.
Cancer therapeutics in particular seemed to suddenly be accelerating, Seiwert said, as new and targeted therapies became available.
Currently, Seiwert is working on unraveling the similarities that seemingly certain disparate cancers share. While he is focused on head and neck squamous cell tumors, Seiwert noted that those tumors are similar not only to lung squamous cell tumors but also to esophageal squamous cell tumors and to bladder squamous cell tumors.
"One of my interests is to look at these cross-tumor biological principles," Seiwert said.
Researchers from France and Russia describe a giant DNA virus that they discovered in a 30,000-year-old permafrost sample from Siberia. The virus, dubbed Pithovirus sibericum, shares morphological features with pandoraviruses, the team notes. But when researchers scrutinized the new virus' 600,000 base genome, they found that its gene content more closely resembles that of icosahedral viruses such as Iridoviruses and Marseillevirus. As such, the virus appears to represent a third type of giant, amoeba-infecting virus, distinct from the very large Megaviridae and Pandoroviruses described recently. "The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health," the study's authors write.
A University of Southern California- and Nara Medical University, Japan-led team took an array-based look at the DNA methylation changes that occur in human intestinal cells in the wake of surgical tissue transplantation. By comparing methylation levels in intestinal epithelial cells before and after surgery to reconstruct a bladder from intestinal tissue, the researchers demonstrate that the intestinal cells in the newly formed "neobladder" take on distinct epigenetic features over time, moving away from their original tissue-specific methylation profiles. "The dynamic resetting of [the] DNA methylome in the neobladder not only implicates local environmental cues in the shaping and maintenance of the epigenome," researchers write, "but also illustrates an unexpected cross-talk between the epigenome and cellular environment."
People on the Move
Hologic has named Eric Compton to the newly-established position of chief operating officer. He most recently served as worldwide president of Johnson & Johnson's Ortho Clinical Diagnostics business. Hologic also named Claus Egstrand its new senior VP and general manager, international. He previously held senior positions at Merck, Stryker, Pfizer Consumer Healthcare, and Pharmacia. In addition, David Harding, who previously served as Hologic's group senior VP and GM of women's health, has been named senior VP of corporate strategy. CFO Glenn Muir, who began serving in that post in 1992, will retire from the firm at the end of November.
SISCAPA Assay Technologies has named Selena Larkin its vice president of marketing and sales. Larkin joins the mass spec assay firm after recently serving as global director of pharmaceutical strategy at Agilent Technologies. She previously held positions at Applied Biosystems/Sciex and Irvine Scientific.
Sequenom announced this week that CEO Harry Hixson plans to retire from that position in June, at the time of the company's stockholder meeting. Current President and Chief Operating Officer William Welch will assume Hixson's position upon his retirement. Hixson will continue to serve as chairman of the firm's board of directors, a title he has held since 2003. Welch also will be nominated to serve on the board at the annual meeting, Sequenom said. Also, CFO Paul Maier also will retire from his job in June, but will continue to work with the company as a consultant. Current VP and Chief Accounting Officer Carolyn Beaver will replace Maier as CFO upon his retirement. She previously was corporate VP and controller of Beckman Coulter. In addition, Dirk van den Boom will be promoted to be chief scientific and strategy officer. He has been with Sequenom since 1998, and he recently was the company's executive VP of R&D and chief technology officer.
Former Life Technologies executive Paul Grossman has joined Telegraph Hill Partners as a venture partner. Grossman previously was head of global strategy and corporate development at Life Tech, and he also held the same position at Invitrogen. Before he joined Invitrogen, Grossman held a variety of leadership roles at Applied Biosystems, including as a research scientist and patent attorney, VP of intellectual property, and VP of strategy and business development.
Through an epigenome-wide association study, researchers have linked DNA methylation at three spots in one gene to body-mass index. Investigators examined the methylation status of nearly 480 people, finding a handful of probes associated with BMI. The researchers confirmed three of those probes — all in intron one of the HIF3A gene — in two additional cohorts. They noted, though, that methylation at these HIF3A sites was likely a consequence rather than a cause of increased BMI.
The FDA Microbiology Devices Panel of the Medical Devices Advisory Committee has recommended first-line use of Roche's cobas HPV test for women 25 years and older to assess their risk of cervical cancer based on the presence of clinically relevant high-risk HPV DNA. If the FDA follows through on the recommendation, the cobas HPV test, which provides genotyping information for HPV 16, 18, and 12 other high-risk HPV types, would be the first HPV test indicated for first-line screening of cervical cancer in the US.
Harvard Medical School and Columbia University have both received grants from the National Institute of Allergy and Infectious Diseases, totaling $12.3 million this year, to create translational research centers to develop molecular diagnostics technologies. Funded under NIAID's Centers of Excellence for Translational Research program, the grants will provide $6.3 million to Columbia and $6 million to HMS this year. Columbia's center could receive a total of $31 million in funding over the full term of the award.