Science & Justice Working Group Meeting
Andro Hsu with discussion by Ted Goldstein and Whitney Boesel
November 9, 2011
Engineering 2, Room 599
4:15-6:15 PM
Andro Hsu (VP of Products at GigaGen and former science writer and policy advisor at 23andMe) will join us for a discussion of what we are learning—both about policy/society and biology—as increasing resources are put into turning the ever growing amounts of genomic information into something of value. Ted Goldstein, PhD candidate at the UCSC Center for Biomolecular Sciences and Engineering, will provide a response to Hsu presentation.
Mark Diekhans: “Art of Genome Browsing”
SJWG Rapporteur Report
14 November 2007
Mark Diekhans, a technician on the Human Genome Browser (HGB) team here at UCSC offered
the SJWG a chance to observe and discuss the browser (http://genome.ucsc.edu). His tour
included an overview of genomes and genome biology, an introduction to the HGB, examples of
the kind of information displayed through the browser, and a demonstration of how to search the
browser. In Mark’s words, the browser is a ‘visualization in reference genome space’ that
organizes data in annotation tracks mapped onto chromosome sequences. Annotation tracks can
be viewed at many different levels, from chromosome to base sequences. There are presently 41
different species displayed on the browser. Access to the browser (designed by Jim Kent at
UCSC in 2000) is freely available to researchers and the public. Mark’s introduction to basic
genomics included a discussion of genes, transposons, single nucleotide polymorphisms, and
short tandem repeats, all of which are important to interpreting the data displayed in the browser.
Mark also shared cautionary case studies about how genomics data can be misinterpreted
(especially by the press), including BRCA1 (‘the breast cancer gene’) and FOXP2 (‘the speech
gene’).
The first point of departure for discussion was the notion of a ‘reference genome.’ The browser
displays comparisons across species specific reference genomes, which stand in as a
representative of a species. The human reference genome is the haploid genome of an
anonymous male donor from Buffalo, NY, and does not in anyway represent an ‘ideal’ human
genome. Comparison across references allows genomics researchers to identify the location of
functional and historical elements by aligning patterns across genomes. Discussion included
concerns about the use of the phrase ‘the human genome’ when the information displayed is
actually ‘a human genome.’ Mark noted that although the reference genome is one person’s,
when an important region is studied there are samples taken from a variety of people to account
for a partial set possible variations. The references for such data are accessible from the browser.
The discussion about reference genomes lead to a discussion concerning how genomics data
might be displayed to represent different kinds of relationships between organisms. As it is
arranged now the browser is most useful for examining evolutionary relationships, particularly
the conservation of certain genes through ancestral histories. Hiram noted that genomics is
primarily about telling evolutionary histories—since every genetic trait must be received from an
ancestor, a genomics perspective is ultimately about ancestry. Donna suggested that there are
other kinds of relationships that are of substantial interest that are interrelated with genomics and
profoundly useful, such as toxicogenomics. Rather than being interested in straightforward
ancestry, a researcher may want to know about the genomics elements of a present
environmental problem. These relationships require a different temporality than what is
available on the browser.