Archives for posts with tag: Genomics

In the 21st century we have an amazing amount of knowledge at our fingertips. This includes the human genome sequence – (most of) the 3,381,944,086 letters of DNA code for a human, known as the human genome sequence. It’s publicly available and you can look it up or download it if you have a computer with internet. Maybe some of us in the developed world are even starting to take it for granted.

The downloadable sequence is just a reference – each one of us has our own unique variation of this standard. Many of us now have reason to find out the sequence of one of our own genes, for example to see if we have inherited a higher than average risk of cancer, or if we carry a gene for a genetic disease. It’s even possible to get your own whole, unique, genome sequenced (at a cost).

In the 1980s the human genome sequence was a dream. Using the technologies available at the time we’d still be sequencing by hand. The Human Genome Project led to a lot of automated sequencing methods being developed – and they’re still being improved, which is still bringing the cost of DNA sequencing down.

This huge project was undertaken by many laboratories across the world. It was intended to be, and has been, a resource for improving health care. It’s not the only sequenced genome. Simpler organisms like viruses and yeasts, which have much smaller genomes, were sequenced before the human genome, and as time goes on we’re getting genome sequences for more and more living things.

So how was the human genome sequenced? There are a range of basic techniques and tools that allow DNA to be manipulated and  read. I’ve put together a Prezi which gives a visual overview of these tools.

Prezi: Tools for DNA discovery and innovation

DNA tools

To see this Prezi with more detailed explanations click on the link above.

DNA can be thought of as a long string of “letters” (nucleotide molecules) strung together. This makes up the code of life and it’s translated into a different language that can make any of the huge variety of proteins, like collagen, haemoglobin, insulin or botox. DNA can be cut, rearranged and joined back together. This makes it very versatile – it can be manipulated. It can be cut up and pasted into different organisms and the host organism will treat it like its own DNA – because the code of life is universal.

Another useful feature of the DNA molecule is that it’s made of two strands which pair together and each one can be made anew from its partner. Thus we can make new DNA in the test tube. One DNA strand can also find its partner so we can find or pick up a whole piece of DNA if we have a  just a small section of its partner.

So these tools for DNA analysis can also be used for our own purposes – for example. to make proteins such as human insulin in massive amounts. You can even make a gene from scratch if you know the code of the protein you want to make. But you’ll still need a live organism to process it into protein for you. Amazing! Diabetics used to rely on pig and cattle insulin, but the human version is better for us!

Cross posted from Fireside Science at SciFund Challenge

Further reading:

https://chromosomesandcancer.com/2013/06/18/the-human-genome-project-and-cancer/

https://chromosomesandcancer.com/2013/07/07/the-last-frontier-of-the-human-genome-sequence-repetitive-dna/

http://www.genome.gov/12011238

The Wellcome Trust’s Sanger Centre has a lot of information, videos and interactive tools that help explain DNA analysis and how the Human Genome was broken down into sections and sequenced. http://www.sanger.ac.uk/about/engagement/yourgenome.html

Advertisements

(This is cross-posted from the Fireside Science blog at SciFund Challenge.)

We care about our health and the health of our loved ones. If only we had explanations and cures for all of humanity’s illnesses. But there are still many diseases that aren’t being researched, even though they cause real and obvious suffering.

Medical research is paid for in a number of ways. The obvious one is the drug companies, where there’s a cost-benefit consideration. I’ll discuss the other options, and how it works in Australia.

The biggest pool of money comes from the government. We have the National Health and Medical Research Council (NHMRC), which runs several grant funding schemes each year. There are also some Fellowships that provide researchers with a secure salary for up to five years. Research grants typically last three years, and they usually include salaries for scientists working on the project. Only 16.9% of Project Grant applications were funded for this year. And the competition gets stiffer every year. So this is clearly not a reliable source of funding for most research wish lists. In the words of the crowdfunding site microryza, “Our system for funding science is broken. Our planet’s biggest funders are so conservative that they fund … only the most obvious ideas. Discoveries that matter are languishing.”

Charitable giving picks up a lot of research that the government doesn’t fund. Besides the work they do supporting patients and their families, some patient advocate groups raise funds for research. There are also private citizens who set up research trusts, and many many more who donate to research. Most of these charities and trusts pull less weight than the government grants, but there are some very large ones based overseas, such as the Wellcome Trust and the Bill & Melinda Gates Foundation.

There’s also a new movement known as crowdfunding. You may have heard of Kickstarter. There are other crowdfunding sites specifically for scientific research. Examples are microryza (now renamed experiment), Petridish, and SciFund Challenge. There have been some remarkable successes like the microbiome project but most projects ask for a modest amount. Researchers are turning to crowdfunding more and more as other sources of funding become harder to get.

So there’s a limited pot of money for research. Who decides what it’s used for? Government grants are hotly contested. One of the tasks of the grant writer is to convince the reviewers that theirs is an important problem and the team has the expertise to solve it. Some charitable trusts have a similar review system, but it can also vary quite a lot and can depend on the wishes of the donors. Crowdfunding cuts out the middle man and it’s the donor who must be convinced that the project is worthwhile.

So, why isn’t there more research into your disease and what can you do about it?

You will need researchers who have an interest in your disease and some funding. Which brings us to awareness. Greater awareness by governments, policy makers, researchers, and doctors who make diagnoses will help your case. Under-recognition of rare diseases is a huge problem which can also be addressed by awareness.

The common and high profile diseases such as cancer get a lot of research dollars. Their severity and impact on the community are obvious. Rare diseases don’t have this advantage. Rare Disease Day is an annual event that advocates for people with diseases, syndromes and conditions that occur in fewer than one in 2,000 people. Rare Disease Day is coming up – most years it falls on the 28th February, but every fourth year or 1,461st day it falls on that rare date – 29th February.

Patient advocate groups that offer research grants can have some influence. They can offer grants that are targeted to a specific disease or question. This can help them find researchers with the appropriate expertise, and attract researchers who are looking for funding. They can use the funds that have been raised specifically to improve the lives of the people they support. Crowdfunding is also a great way to target donors who are keen to support the cause.

About 80% of rare diseases are caused by genetic errors. Humans have over 3,000,000,000 letters in their genetic makeup, and these spell out over 20,000 pairs of genes. Many genetic diseases are caused by a one letter error in one of these genes. The human DNA sequence is now mostly known, so it’s possible to read the DNA sequence of the patient and compare it to a standard to find a needle-in-a-haystack DNA error. Unfortunately not all genetic diseases are that straightforward – but it’s a start.

Recently there have been some heart-warming examples of very rare but debilitating diseases for which the causes have been found with the help of sequencing and a persistent parent, being in the right place at the right time, or scientists who were looking for a problem to solve. These are some of the good news stories of modern genetics that are starting to make an impact on rare diseases.

If you want to help make a difference my advice is to support your disease’s patient advocate group, fundraise and lobby for research. If there isn’t a support group for your disease, you could start one. If your disease is rare, Rare Disease Day is there to help. And anyone can help raise awareness about a disease. Better awareness brings better understanding.

LINKS TO PERSONAL GENOME STORIES

Cracking the code – transcript of the Australian Story episode on ABC TV. A father’s quest to find the gene mutation causing his son’s disease.

Genome maps solve medical mystery for Calif. twins – Shots – Health news from NPR.

We gained hope.” The story of Lilly Grossman’s genome – National Geographic’s Phenomena – Not Exactly Rocket Science

James Lupski’s Research into His Disease Paved Way Toward Personalized Medicine – Quest (MDA Magazine Online – Fighting Muscle Disease)

The Solution to Diagnostic Delay May Be Closer Than We Think – blog post by the National Organization for Rare Disorders arguing that a rare disease app may help doctors diagnose rare diseases: “…most… rare diseases are unfamiliar to doctors… When doctors are unable to explain patients’ symptoms — as they are for at least three years in the majority of rare disease cases — psychiatric diagnosis is made by default.”

When it was initiated by the US Department of Energy in 1987, the Human Genome Project was an ambitious, some said impossible, endeavour.  It was all about producing a representative readout of the human genome – that is, the whole set of human DNA.

At the time DNA was read (sequenced) manually – scientists read each letter of the code off an X-ray film. One by one genes were laboriously found and sequenced. Finding and characterising a gene in this way was a whole PhD project, if you got lucky and actually found the gene (finding a gene by family studies was harder than starting with a known protein).

Humans have some 3,000,000,000 letters (base pairs) in their genome, so a faster approach was needed to get the project finished in the planned 15 years.

The Human Genome Project encouraged the development of much faster automated sequencing. I attended the 1991 Cold Spring Harbor Genome Mapping and Sequencing Meeting and there were several examples of exciting new automated sequencing prototypes, which used a range of different approaches.

photo 2

Abstract book from the 1991 Genome Mapping and Sequencing Cold Spring Harbor meeting.
Sample abstracts: “Capillary gel electrophoresis for DNA sequencing – comparison of three different approaches” (HP Swedlow et al); “Library of 256 hexamers, degenerate at two positions (5′-NNXXXX-3′), can create all possible 12-mer primers for applications in high-volulme DNA -sequencing strategies” (D.Shoemaker et al)

Now we can take it for granted that we can look up a gene on the internet. Having a human genome sequence was going to make a big contribution to health care. It is already helping, and will play a bigger role as we learn more about what roles the various genes play. For example working out what genes are playing a role in cancer will become more routine.

We can already do a lot for some cancer patients by doing genetic tests on their cancer. There are many categories of leukaemia that have a very specific type of DNA abnormality, and knowing what gene is involved can help diagnose and treat the disease appropriately.

Chromosome abnormalities helped make some of the earliest cancer gene discoveries. That’s because the gene abnormalities that cause some cancers are caused by microscopically visible changes to the chromosomes, which pinpoint the cancer gene. The poster child for this is chronic myeloid leukaemia. Most cases of CML have a chromosome abnormality known as the Philadelphia translocation. In fact this was the first cancer chromosome abnormality to be discovered. Imatinib (Glivec/Gleevec/STI-571) was one of the first targeted cancer drugs. Designed to lock onto the molecule produced by the cancer gene, it targets the leukaemia cells containing the Philadelphia chromosome. It’s made a huge improvement to the outlook for CML patients.

But for most cancers we’re not so lucky – the cancer-causing genes are not usually so obvious or easy to identify. Most cancers have their own individual combination of genetic errors, and what’s more, the genome changes as the cancer grows more aggressive and spreads. Sequencing of whole cancer genomes could become standard practice in cancer treatment, as a way of understanding each cancer and selecting treatment that targets its specific genetic changes. First we will need to be able to read a complete genome quickly and cheaply. We’re not there yet. But we’re on the way. Compared to 15 years for one representative genome, that’s impressive.

Next time: The Human Genome Project was said to be complete in 2003, in time for the 50th anniversary of the discovery of the structure of DNA. Actually it’s still not finished. Most of the gaps are regions that are very relevant to cancer.

Wellcome_genome_bookcase 2

The first printout of the human genome to be presented as a series of books, displayed in the ‘Medicine Now’ room at the Wellcome Collection, London. The 3.4 billion units of DNA code are transcribed into more than a hundred volumes, each a thousand pages long, in type so small as to be barely legible. From Ross London et al en.wikipedia.

Angelina Jolie decided to have a double mastectomy because she inherited a high risk of breast cancer. What’s remarkable is that all of a sudden people are questioning whether they should be investigating their own cancer risk. Cancer services are fielding many more queries about cancer testing than they were before her announcement. (20th June: I posted this ten days ago, and I’ve just updated the title in response to what has become known as the “Angelina effect”.  Cancer Council Victoria has just announced a 1033% increase in the number of calls to its helpline.)  This is despite the fact that what we know about breast cancer risk that led to Ms Jolie’s decision has already been publicly available for many years. Clearly it was not out there in a way that people took much notice of.

Better communication of science will prevent people from missing or misunderstanding  important information like that.

Is cancer the most common genetic disease? According to The Cancer Genome Project website it is. This might sound scary. Does it mean you have a high risk of cancer if one of your parent has had it? Not necessarily. “Cancer genetics” means one thing to most people and another to cancer scientists. To understand all this we need to understand something about genes and the the role they play.

Genetics is usually understood to mean the characteristics that you inherit from your parents. These characteristics are encoded in our genes,  which are instructions written in a special language called DNA. Every cell has a copy of the set of instructions, and can read them. Genes control our physical features, and the way our bodies’ function, for example how they grow. Genes in the germ cells (eggs and sperm) are passed on from parent to child. Genes in the embryo are passed on to every new cell as we grow. The new cells include eggs and sperm, and their genes are passed on again to the next generation.

The genes can get damaged – this can happen by chance, or it can be caused by environmental factors. Usually this damage is not a problem for a number of reasons. But sometimes the damage is a step in the development of cancer. Usually more than one of these cancerous genetic changes has to occur before cancer is triggered. For breast cancer to develop, these errors need to occur together in the same breast cell.  So cancer can arise in any part of the body, but one of these faulty genes is only inherited if it’s in a germ cell.

If the faulty cancer-promoting genes are inherited, cancer is more likely, because fewer additional gene errors are needed before cancer is triggered. Ms Jolie is reported to have a faulty or mutated BRCA gene. A mutation in a woman’s BRCA gene (BRCA1 or BRCA2) means a 60% lifetime risk of breast cancer, compared to a 12% risk in women without the mutation (National Cancer Institute).

What’s a genome anyway? Scientists studying the genes talk about the genome. This simply means all the genes in an organism – a plant, animal, microbe, you or me. And if you think small-scale, every cell has a genome. Genomics is the study of a genome, be it  the whole organism or a single cell. So “genomics” is really a less ambiguous term than “genetics” when you’re talking about cancer, but to most people it’s jargon. I think this will change as genomics becomes a much more prominent part of health care, including cancer treatment. So to answer the question posed above, yes, cancer is the most common genetic disease, but not in the generally understood sense.

There’s a huge amount of research behind our knowledge of BRCA genes and our ability to use this information to prevent or treat cancer. Cancer is a very diverse disease and we are nowhere near understanding all the gene errors behind all the various types of cancer. The more we discover the better equipped we will be to prevent, detect and cure cancer.

(With thanks to Qian Yu for helpful comments)