Author: Rose Miyatsu
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Abstract: We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous…
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Biology’s moonshot: The mission to decode the DNA of all life
A new plan to sequence all Earth’s animals and plants could lead to medical and material advances that dwarf even what the Human Genome Project has achieved April 4, 2018 By Alice Klein BOB MURPHY has had some close shaves. He once found a deadly viper slithering into his sleeping bag in a Southeast Asian jungle.…
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Jenny Reardon among scholars speaking out on genomics and race
April 04, 2018 By Jennifer McNulty A professor of genetics at Harvard kicked up quite a storm recently when he published an opinion piece in the New York Times about genetics and race. Entitled, “How Genetics is Changing Our Understanding of ‘Race,’” the piece by David Reich provoked a swift response from scholars around the globe, including Jenny Reardon, a…
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DAN HELLER (DANM ’13) RECEIVES ALUMNI AWARD / STARTUP RAISES $24.5 MILLION
Thursday, April 27, 2017 – 2:10pm Dan Heller, DANM MFA 2013, and CEO of Santa Cruz start-up, Two Pore Guys, Inc., has been awarded the 2017 Distinguished Graduate Student Alumni Award for the Arts Division. On top of that, Two Pore Guys recently closed Series A venture financing of $24.5 million led by Khosla Ventures, for their innovative…
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UCSC Paleogenomics Lab
The Paleogenomics Lab is a joint venture between Beth Shapiro and Richard (Ed) Green. Their research focuses on the evolutionary and ecological questions relating to the study of genomics. Learn more about the UCSC Paleogenomics Lab here.
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Treehouse Childhood Cancer Initiative
The Treehouse Childhood Cancer Initiative was established to analyze genomic data of children with cancer in the context of large data sets of both pediatric and adult cancers. This allows researchers to identify situations where an available drug is predicted to work for a given patient’s tumor. Treehouse promotes the sharing of pediatric cancer genomic…
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Open Source, Open Data
Data Sharing: Fast Forward Consent Chair: Nazneen Rahman (The Institute of Cancer Research, The Royal Marsden NHS Foundation Trust) For the rest of the 4th Plenary Meeting – October 18th, check out the summaries found in Global Alliance for Genomics & Health. David Haussler (University of California, Santa Cruz) reviewed the technical process and progress of GA4GH toward…
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BRCA Exchange
We are developing the BRCA Exchange, a comprehensive, global data repository to catalogue variation within the BRCA genes and to collect individual-level evidence for their classification. The scientific and medical communities have a tremendous and urgent need for a comprehensive data store of variants in the BRCA1 and 2 genes. Variation in these genes can…
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Vertebrate Genome Project/ Genome 10K
The vertebrate evolutionary treeThe Vertebrate Genome Project/ Genome 10K aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity…
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Global Alliance for Genomics & Health Integration Group
The Global Alliance for Genomics and Health (GA4GH) is an international effort to promote, foster and standardise secure, ethical, privacy preserving sharing of genomic information for the betterment of global health outcomes. It has many, many organizations involved, all recognising the importance of its mission, however it is largely a volunteer effort. To help ensure…
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High Throughput Genomics Group
Genomics is in transition. The growth in data—driven by the need for vast sample sizes to gain statistical significance and the explosion of clinical sequencing—is far outpacing Moore’s law. Large projects like The Cancer Genome Atlas have generated petabyte scale datasets that very few groups have the capacity to analyze independently. Looking forward, improvements in…
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Computational Nanopore Genomics
Nanopore technology is emerging as one of the leading contenders for next generation sequencing. The concept of nanopore sequencing was envisioned in the early 1990’s by David Deamer (UC Santa Cruz) and Daniel Branton (Harvard). The recent commercialization of the technology, particularly the Oxford Nanopore’s disruptive MinION, has ignited the field. In collaboration with the…