https://en.wikipedia.org/wiki/Whole_genome_sequencing
https://en.wikipedia.org/wiki/DNA_sequencing#High-throughput_methods
https://en.wikipedia.org/wiki/Laboratory_developed_test#Direct-to-consumer
https://en.wikipedia.org/wiki/Genetic_testing#Direct-to-consumer_genetic_testing
https://en.wikipedia.org/wiki/Personalized_medicine
https://en.wikipedia.org/wiki/Personal_genomics
This is the part that is contentious.
There has been much debate about whether people should be able to see
their own data.
Many institutions have the stance that:
“People are not smart enough to interpret their own health data,
and could not possible know what is good for themselves.”
The American Medical Association, Wikipedia, and others enforce such
policies:
https://en.wikipedia.org/wiki/
How to get and interpret personal direct-to-consumer (DTC) whole genome sequencing (WGS)?
Chances are, at least several of you will find a major recessive
disease,
and many others will see subtler negative association with SNPs present
in your genomes.
One of the tenets of AI is that no rational agent can have too much
information.
Are you a rational agent?
The above statement assumes the rational agent is the only one with the
information,
and does not consider the value of others having such information.
Will these companies share your information; will they store it;
where are their servers; do they upload or mail you an SD card,
etc.?
Your health, your childrens’ health, curiosity, research…
Time, money, anxiety, discrimination, mis-interpretation leads to irrational behavior…
Choose whether you want to get sequencing.
Get data from other people to explore!
https://www.personalgenomes.org
https://en.wikipedia.org/wiki/Personal_Genome_Project
See below:
https://isogg.org/wiki/List_of_DNA_testing_companies
Without physician involvement (recommended):
https://www.yseq.net/
Germany has better privacy than EU itself.
https://www.fullgenomes.com
Known compatible formats with interpretation tools, USA based lab,
has varying quality levels, depending on how much you want to pay.
https://us.dantelabs.com/
EU maybe better for privacy than US.
https://24genetics.com/en/whole-genome-sequencing
EU maybe better for privacy than US.
With physician involvement (not recommended):
http://www.genos.co/
http://www.suregenomics.com/
https://www.veritasgenetics.com/
You can choose how much privacy emphasis you prefer.
If it is important to you that others not have your genome
information,
then there are steps you can take (but you can just skip if that’s not
important to you).
Discussed in class only, take notes or ask after class if you are
interested.
../../Networking/Content/13-API.html
Local software
* IGV,Integrative Genomics Viewer by the Broad Institute; open source.
http://software.broadinstitute.org/software/igv/
* IGB, Integrated Genome Browser from the University of North Caroline,
Charlotte; open source. http://bioviz.org/igb/
* Artemis by the Wellcome Trust Sanger Institute. One of the few
browsers that can handle GenBank and EMBL formats! Open source. http://www.sanger.ac.uk/science/tools/artemis
* Tablet from the James Hutton Institute. Closed source? https://ics.hutton.ac.uk/tablet/
* SeqMonk A tool to visualise and analyse high throughput RNA-Seq
alignments. Closed source? http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
* Samtools simple browser; open source. http://www.htslib.org/
Web-based
* UCSC Genome/Table Browser from the University of California at Santa
Cruz. Open source. https://genome.ucsc.edu/ and then https://genome.ucsc.edu/cgi-bin/hgGateway
* Ensembl Genome Browser from the partnership of the European
Bioinformatics Institute and the Wellcome Trust Sanger Institute
* Run-your own web-server on localhost (isolated or anonymized if
preferred)
* GBrowse: Generic Genome Browser a combination of database and
interactive web pages for manipulating and displaying annotations on
genomes. https://github.com/GMOD/GBrowse
* JBrowse an embeddable genome browser built completely with JavaScript
and HTML5, with optional run-once data formatting tools written in Perl.
http://jbrowse.org/
* GBiB: Genome Browser in a box is a “virtual machine” of the entire
UCSC Genome Browser website that is designed to run on most PCs. An
alternative to look into may be “track hubs”. https://genome.ucsc.edu/goldenpath/help/gbib.html
Real-time genomic analysis, scientific and clinical reports.
http://iobio.io/
http://evidence.pgp-hms.org
* Using an example full genome (from George M Church)
* http://arep.med.harvard.edu/gmc/
* https://en.wikipedia.org/wiki/George_M._Church
* https://my.pgp-hms.org/profile/hu43860C
* http://evidence.pgp-hms.org/genomes?display_genome_id=09b04be3309715d773b2a2789799f017ea27aa0e
https://www.promethease.com
* https://files.snpedia.com/reports/promethease_data/Genos_example1_ui2.html
https://opensnp.org/
* https://opensnp.org/genotypes
http://www.omim.org/ for more manual research on whatever you find, which links to UCSC genome browser
Discussion points
What % genes versus % environment is a phenotype?
E.g., intelligence?
Phenotype-genotype associations to review: