Genetics

The Times newspaper has published a front-page story revealing that the Duke of Cambridge, Prince William, and his brother Prince Harry share some Indian ancestry via their mother, based on DNA analysis of distant cousins. ? This in itself is not a particularly controversial revelation &ndash ...

Quick post here ... Some news stories and posts I am checking out today in relation to the UC Davis ADVANCE project in which I am involved. National Geographic: In Her Words: Sylvia Earle on Women in Science – News Watch NY Times Japan's 'Science Women' Seek an Identity NBC News:The Whole World Celebrates 50 Years of Women in Spaceflight Gulf Today: Arab women in science get fellowship boost NY Times: The Unspoken Stigma of Workplace Flexibility -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------

For many many years I have been raising a key questions in relation to open access publishing - how can we measure how open someone's publications are. Ideally we would have a way of measuring this in some sort of index. A few years ago I looked around and asked around and did not find anything out there of obvious direct relevance to what I wanted so I started mapping out ways to do this. When Aaron Swartz died I started drafting some ideas on this topic. Here is what I wrote (in January 2013) but never posted: With the death of Aaron Swartz on Friday there has been much talk of people posting their articles online (a short term solution) and moving more towards openaccess publishing (a long term solution). One key component of the move to more openaccess publishing will be assessing people on just how good a job they are doing of sharing their academic work. I have looked around the interwebs to see if there is some existing metric for this and I could not find one. So I have decided to develop one - which I call the Swartz Openness Index (SOI). Let A = # of objects being assessed (could be publications, data sets, software, or all of these together). Let B = # of objects that are released to the commons with a broad, open license. A simple (and simplistic) metric could be simply OI = B / A This is a decent start but misses out on the degree of openness of different objects. So a more useful metric might be the one below. A and B as above. Let C = # of objects available free of charge but not openly OI = ( B + (C/D) ) / A where D is the "penalty" for making material in C not openly available This still seems not detailed enough. A more detailed approach might be to weight diverse aspects of the openness of the objects. Consider for example the "Open Access Spectrum." This has divided objects (publications in this case) into six categories in terms of potential openness: reader rights, reuse rights, copyrights, author posting rights, automatic posting, and machine readability. And each of these is given different categories that assess the level of openness. Seems like a useful parsing in ways. Alas, since bizarrely the OAS is released under a somewhat restrictive CC BY-NC-ND license I cannot technically make derivatives of it. So I will not. Mostly because I am pissed at PLoS and SPARC for releasing something in this way. Inane. But I can make my own openness spectrum. And then I stopped writing because I was so pissed off at PLOS and SPARC for making something like this and then restricting it's use. I had a heated discussion with people from PLOS and SPARC about this but not sure if they updated their policy. Regardless, the concept of an Openness Index of some kind fell out of my head after this buzzkill. And it only just now came back to me. (Though I note - I did not find the Draft post I made until AFTER I wrote the rest of this post below ... ). To get some measure of openness in publications maybe a simple metric would be useful. Something like the following P = # of publications A = # of fully open access papers OI = Openness index A simple OI would be OI = 100 * A/P However, one might want to account for relative levels of openness in this metric. For example AR = # of papers with a open but somewhat restricted license F = # of papers that are freely available but not with an open license C = some measure of how cheap the non freely available papers are And so on. Given that I am not into library science myself and not really familiar with playing around with this type of data I thought a much simpler metric would be to just go to Pubmed (which of course works only for publications in the arenas covered by Pubmed). From Pubmed one can pull out some simple data. # of publications (for a person or Institution) # of those publications in PubMed Central (a measure of free ava

For the next week or so, 23andMe is pausing updates to the DNA Relatives feature.  This feature provides a list of genetic matches and estimates the range of relationship. According to this week’s 23andMe update entitled “Release Notes: 7 June 2013,” (you must log in to view), “The computation time for DNA Relatives and Ancestry Composition has been growing.” Going into greater detail at “DNA Relatives computations temporarily on hold,” 23andMe explains that due to the increased computational time, and in an effort to reduce the time it takes to generate DNA Relatives matches, updates are paused.  Accordingly, “[t]his means that you won’t be receiving new matches to your existing DNA Relatives list, and if you haven’t received your matches yet there may be some additional waiting time.” It sounds as though this temporary pause will ultimately lead to faster results for 23andMe customers. The full message is below: “DNA Relatives computations temporarily on hold” Posted by Christine M. in Relative Finder Hi everyone, As Mike mentioned in the June 7th Release Notes, the computation time for DNA Relatives has been growing. Part of the effort to reduce the time it takes to generate DNA Relatives matches has required us to pause updates for this feature for the time being. This means that you won’t be receiving new matches to your existing DNA Relatives list, and if you haven’t received your matches yet there may be some additional waiting time. While putting these computations on pause was the best option available while the update is in progress, we understand that it’s not ideal and we appreciate your patience. We expect to re-enable updates to DNA Relatives by the end of next week, June 21st. I will share updates on this thread as necessary. Thanks, Christine Jun 13, 2013 This was brought to my attention by Larry Vick via the ISOGG mailing list.

The US Supreme Court has ruled unanimously that the patents held by Myriad Genetics Inc. for the BRCA1 and BRCA2 gene sequences are invalid, on the basis that they are a product of nature. ? Justice Thomas wrote: “A naturally occurring DNA segment is a product of nature and not patent e ...

The use of microbes in art projects continues to spread. Here is another example: Bioluminescent art: Beautiful bacteria glow in the dark | MNN - Mother Nature Network. The article discusses the Bioglyphs project which involved "some microbiology training, imagination, and a lot of petri dishes." Definitely worth checking out ... -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------

As I have posted about before - I am involved in the UC Davis ADVANCE project funded by NSF. From the project website: UC Davis ADVANCE is a newly funded Institutional Transformation grant that began in September of 2012. Our program is supported by the National Science Foundation’s ADVANCE Program which aims to increase the participation and advancement of women in academic science and engineering careers. My role in this project is as a member (and now Co-Chair) of one of the "Policies and Practices Review Initiative" Committee. As part of my work on this committee I am trying to read various papers on related topics. And I figured I would simultaneously post about these papers as much as I can because it would be great to get a broader discussion going on these topics. So today I am reading the following:CSHE - Developing Graduate Students of Color for the Professoriate in Science, Technology, Engineering, and Mathematics (STEM) which I was pointed to in our Committee meeting yesterday. It is quite interesting. It is by Anne MacLachlan from the Center for Studies in Higher Education at UC Berkeley. The abstract: This paper presents part of the results of a completed study entitled A Longitudinal Study of Minority Ph.D.s from 1980-1990: Progress and Outcomes in Science and Engineering at the University of California during Graduate School and Professional Life. It focuses particularly on the graduate school experience and degree of preparation for the professoriate of African American doctoral students in the sciences and engineering, and presents the results of a survey of 33 African American STEM Ph.D.s from the University of California earned between 1980-1990. Relationships with thesis advisors and principal investigators are evaluated by the study participants in fifteen specific areas from highly-ranked intellectual development to low-ranked training in grant writing. Deficits in training and socialization are discussed along with the tension between being both an African American and a graduate student. Career choices and outcomes are presented. These findings, in conjunction with current analyses of graduate education in STEM, suggest ways in which graduate training for all could be improved. Lots of interesting information in there. Perhaps most important for my current goals is what she describes at the end in terms of a Proposed Development Program. She starts this section by commenting on the general situation in terms of training scientists in the US today. She then identifies what she refers to a "discontinuities" in federal and local policy which can hinder "developing faculty of color." These include "compartmentalized, externally mandated sets of programs" and the "nature of Ph.D. training". Of the 33 Ph.D.s surveyed in the study, nearly all of them recommended diversity training for faculty. They also recommend better laying out of expectations and requirements for students and more involvement of current faculty in recruiting. They also made many recommendations for improving the life of current students of color. Anyway - a lot of this material and the concepts involved are bit new to me so I am still digesting the article. But I thought I would share it with others in the hope that this will help catalyze more open discussion of issues involved women and underrepresented minorities in STEM fields. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------

DNATraits, a division of Houston-based genomics and genetics testing company Gene By Gene, Ltd., (parent company of Family Tree DNA) just announced a press release regarding today’s decision in Association for Molecular Pathology, et al. v. Myriad Genetics, Inc. patent case regarding the human BRCA1 and BRCA2 genes From the press release:   Supreme Court Ruling Today Allows DNATraits to Offer Low Cost BRCA Breast and Ovarian Cancer Gene Testing in U.S. In effort to increase access to potentially lifesaving BRCA1 and BRCA2 tests, DNATraits can now offer tests for $995, a fraction of the cost of similar tests prior to the court decision HOUSTON — Jun. 13, 2013 – Thanks to today’s U.S. Supreme Court decision opening the door to greater access to genetic medicine by American patients and their health care providers, testing for genes specifically linked to breast, ovarian and other cancers will now be more widely available and at a lower cost than ever before. DNATraits, a division of Houston-based genomics and genetics testing company Gene By Gene, Ltd., announced today that it will offer testing for the BRCA1 and BRCA2 genes in the United States for $995.  Prior to today’s unanimous Supreme Court ruling, when exorbitant licensing fees kept DNATraits and others from offering BRCA gene tests in the United States, the cost for such tests was around $4,000. “We’re pleased to make this important testing more widely available and accessible in the United States,” said Gene By Gene President Bennett Greenspan.  “Our highly automated CLIA-registered lab and efficient processes enable us to make genetic and genomic testing more affordable and accessible to more individuals, in the U.S. and worldwide.  And that’s our company’s mission, in a nutshell.” The company’s announcement about the tests, which gained national attention when actress Angelina Jolie courageously revealed in May that being a BRCA1 carrier was among the factors in her decision to have a preventive double mastectomy, comes after today’s Supreme Court ruling in “Association For Molecular Pathology v. Myriad Genetics.” “We commend the Supreme Court for opening the door to greater technological innovation and access to genetic tools that promise to save and improve the quality of human lives in the United States,” Greenspan added.  “It’s critical that as an industry we are able to continue to engage in healthy competition to drive down the costs of these tests – because as more individuals have access to and undergo them, the more information we’ll have about many serious diseases that eventually may lead to cures.” DNATraits has processed testing for the BRCA1 and BRCA2 genes for individuals living outside the U.S. since 2012.  Those genes are processed using traditional Sanger DNA sequencing, which is considered the gold standard for DNA analysis, at the company’s Genomic Research Center in Houston, a CLIA-registered lab which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations globally. In addition to the BRCA gene tests, DNATraits offers a pre-natal array that covers 111 population specific diseases, as well as other not population-specific diseases, like Duchene Muscular Dystrophy. Customer Inquiries Individuals interested in learning more about either the BRCA1 or BRCA2 tests should ask their doctors for more information.  They and their health care providers can also visit the company’s website, www.dnatraits.com, or call (713) 868-1438 for more information. About Gene By Gene, Ltd. Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity.  Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago.  Gene by Gene is CLIA registered a

Recently I saw one of those presentations that seem common in the era of next-generation sequencing: the kind where they put up a list of genes that were variant or mutated or significant in a sequenced cohort. A glance at the list tells me that there are some true positives — one of the classic [...]

To receive our monthly round-up by email please register?here?(also gives you access to our Resources section).Go to monthly round-up