Bio-Hackers Pore Through A Child’s DNA For The Source of A Mysterious Disease | TechCrunch

"When Max Good was born, it was clear that something was off. At first, he was a colicky baby. But then he wouldn’t make eye contact, revealing that he was almost 100 percent blind at birth. Occasionally, he would have seizures. Then feeding became so impossible and difficult that his parents, Paul and Janis, eventually had to insert a tube up his nose.  Initially, doctors gave Max a cerebral palsy diagnosis. But cerebral palsy captures a set of symptoms or movement disorders that arise from damage to the motor control centers of the brain. It doesn’t describe an exact cause. It’s like how the word “cancer” actually describes a multitude of ways in which normal cell death and division break down for different kinds of cells.  'I’m going to live for decades with this kid. He’s my son. I have to deal with whatever fate throws at us,” said Paul. “But I don’t like the idea of not knowing what this is.'  So after running tests for years — MRIs, EKGs, metabolic testing, you name it — Paul Good decided to explore Max’s DNA on the recommendation of his brother Otavio.  With sequencing costs falling faster than Moore’s Law would suggest, it’s becoming possible for people to get their entire genomes sequenced for a few thousand dollars. In fact, Illumina, the leading company the in the space, announced a machine a few weeks ago that could bring full sequencing costs down to the symbolic milestone of $1,000. It’s important to stress that full sequencing is different from the tests that well-publicized companies like 23andMe offer, which are SNP (single nucleotide polymorphism) tests that examine only small parts of person’s genome.  The dirt-cheap costs mean that it’s possible for computer scientists and hackers to go and literally sort through gigabytes and gigabytes of a person’s raw genomic data. This code is made up of strings of As, Ts, Cs and Gs, the four nucleobases found within DNA. It opens the next challenge: how do you leverage computer science, statistics and mathematics to make sense of this new flood of data?  ... To put it lightly, Rahman and Otavio Good are a little bit mad scientist crazy. Otavio Goodhad a drone deliver a ring to his wedding ceremony, won a DARPA challenge with his friends and wife to build a program that could put shredded pieces of paper back together and made Word Lens, that augmented reality app that uses computer vision to translate texts in other languages on your phone’s screen.  The pair got Max and his parents each exome sequenced. (Exome sequencing is more comprehensive than 23andMe’s SNP tests, but still isn’t as exhaustive as whole genome sequencing.) They paid $7,000 to a company in Southern California called Ambry Genetics to test Max twice and get his parents’ data ...  When you get exome sequenced, you don’t get back a long, uninterrupted string of 3 billion base pairs, which is roughly the normal length of the human genome. Max’s sequencing tests cut his DNA into tiny, little strips that were each 130 base pairs long. It then became a big data problem to go and put them all back together. For statistical purposes, Rahman and Otavio Good wanted 30 overlaps to ensure that one strip accurately led to another.  Then the two of them built software that pieced together Max’s strips and then compared his data against that of his parents and the Human Reference Genome. The reference genome is a mosaic of DNA data from volunteers put together by the National Institutes of Health. It’s supposed to be an 'average' of sorts and the 38th or latest version was released just before Christmas ... To try and figure out which one of Max’s mutations might lead to serious diseases, Rahman and Otavio Good have run an additional library against their data. They’re using the Kyoto Encyclopedia of Genes and Genomes, which is a painstakingly curated database of genes and the proteins they code for that’s been supported by the Japanese government for the last two decades.  From that, they’ve generated a list of 100 or so diseases that might match Max’s mutations with the Kyoto database. The most helpful part of the process is how they’ve been able to rule out genetic disorders that don’t match Max’s data ... "