CheckMate

Client: Illumina Contact: "Oldham, Scott" <soldham@illumina.com>

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.

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.

Appendix: Illumina stores variant calls resulting from the sequencing of a genome in a standard format (gVCF) file. 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/).