From Computer Laboratory Group Design Projects
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| contact Scott Oldham -(soldham@illumina.com) | | contact Scott Oldham -(soldham@illumina.com) |
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| [[CheckMate]] | | * [[CheckMate]] |
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| Personal genome sequencing is now available to the masses! An individual human's genome sequence contains 3 billion bases. It can be represented as either a string of characters or as a graph showing where the sequence deviates from a standard, reference genome. Your task is to (1) write a tool to filter/compress such a file into a representation of the genetic status for a (provided) selection of serious diseases of an individual, such that it can be stored on a Raspberry Pi or smartphone, and (2) write a Raspberry Pi or smartphone app that can securely communicate with another to establish whether the two individuals represented share genetic status of any of the diseases considered.
| | * [[Genomes are fun!]] |
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| For bonus points: The genetic details of one individual should not be revealed to the other individual - beyond reporting that the two individuals do or do not share genetic status for one or more diseases.
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| Appendix: Illumina stores variant calls resulting from the sequencing of a genome in a standard format (gVCF) file.
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| Most healthy individuals are carriers of one or more mutations that, if present in two copies (i.e. inherited from both mother and father), would result in a serious disorder (eg 1 in 29 Caucasian Americans carries one mutation in the cystic fibrosis gene : http://www.cff.org/AboutCF/Testing/Genetics/GeneticCarrierTest/).
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| [[Genomes are fun!]] | |
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| Design and implement a game (on iOs and/or Android) to teach the user about genomes or genomic sequencing, targeted to a GCSE or A level science student. The game should have a strong social element to it.
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| One suggested game could be bacterial genetics, where each user has a 'pet bacterium' with certain continuous characteristics, eg shape, size, ability to survive on a wide range of foodstuffs, resistance to antibiotics. Bacteria can exchange parts of their sequence (the social aspect) and the challenge is to evolve the overall fitness of your pet bacterium by interaction and exchange with others. The user can select which small part of the bacterial genome to exchange with a friend. Eventually users will be able to work out which parts of the bacterial genome define which of the characteristics and move up the leaderboard of 'fit bacteria'. (mobile apps, graphics, social networks, no background in biology required)
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Revision as of 14:57, 28 August 2013
contact Scott Oldham -(soldham@illumina.com)
