Month: August 2016

The Journey

Getting results in the 100,000 Genomes Project – The Journey

The first attempt to sequence a whole human genome took 13 years – all 3 billion letters of the genetic code. Super fast new technology means this can be done in as little as 24 hours today.

In practice, because we batch genomes together for efficiency, it takes us 3 days to sequence a whole genome.

But sequencing is only the beginning.

Looking for a needle in a haystack

When we look at your genome, we are looking for a needle – a glitch – in a vast haystack. The first thing we need to do is make the haystack a bit smaller.

Luckily human genomes are 99.8% the same. But that’s still around 4 million potential differences, most of which are healthy variations that make us the individuals we are.

Sequencing your genome produces two files of info. One is the raw data – all six billion letters. The other is what’s called a variant call file. That’s the 4 million. This is the ‘small’ haystack we now work with.

The process so far has largely been automatic. (Though at the time we started this project, no-one in the world had sequenced 100,000 whole genomes – and we’ve made something sound easy that even 5 years ago would have been thought impossible. Hats off to Illumina who do this for us in Cambridge.)

Next comes the bit that takes the time.

Call in the Bioinformaticians

Bioinformaticians – scientists who are brilliant at organising information and spotting patterns – trawl through the 4 million, looking for the glitches that might possibly account for someone’s symptoms. They decipher how each one might affect a person and pull from the many, many hundreds of potential ‘needles’ – changes that might possibly be responsible for a problem. This bit is called ‘annotation’.

But they’ve still got hundreds and hundreds of potential suspect glitches. A small haybale’s worth.

“Trawling through the 4 million used to take a year or more.”

Some of these now get discarded thanks to a filtering system which uses special tools that can access huge databases of knowledge. Out for instance go changes where there’s good evidence that they’re commonly found in the population and don’t cause a problem. Out also go changes that don’t fit the disease in your family.

National Training Consent Day

Join us in September to learn the skills and knowledge required to recruit and consent patients to the 100,000 Genomes Project.

HEE’s Genomics Education Programme in conjunction with the Birmingham Women’s Hospital Clinical Genetics unit and the West Midlands Genomic Medicine Centre (GMC) education team will be hosting a National Consent Training Day on Tuesday 20th September in central Birmingham.

The aim of the day is to introduce and demonstrate the use of a blended learning package that is designed to equip health professionals with the skills and knowledge required to recruit and consent patients to the 100,000 Genomes Project.

The package incorporates the Genomics Education Programme’s ‘Preparing for the consent conversation’ online training course and training materials that can be used in face-to-face sessions.

We would like to invite individuals from each Genomic Medicine Centre (approximately three from each centre) to attend this event. Ideally these representatives will be the individuals who will provide consent training within their GMC. Please email Charlotte Szczepanik if you would like more information or with the details of who will be attending. The location of the meeting will be confirmed in the coming weeks.