“We’re all mutants”, that’s the conclusion of a study by 16 scientists from various countries who used a new method called direct sequencing to count individual differences among 10 million units (nucleotides) of DNA belonging to each of two men living in the same Chinese village who shared an ancestor 200 years ago.
The study was the work of Dr Yali Xue from the Wellcome Trust Sanger Institute in Hinxton, Cambridgeshire, UK, and colleagues, and was published online on 27 August in the journal Current Biology.
Xue was one of the leaders of the project which also included other researchers from the Wellcome Trust Sanger Institute and also from the Chinese People’s Liberation Army General Hospital in Beijing, and the Beijing Genomics Institute at Shenzhen, China.
“Understanding the key process of human mutation is important for many aspects of medical genetics and human evolution,” wrote the authors.
We have known for a long time that mutations occur occasionally in each individual, but have had to guess exactly how often. Because mutations can lead directly to diseases like cancer, we need better measurements of mutation rates, so we can test ways to reduce mutations, for example.
Now, thanks to advances in the technology for reading DNA and this new research, we can begin to do this.
Xue and colleagues used new sequencing technology to measure the number of nucleotide differences in the DNA code of the Y chromosome between two men separated by 13 generations.
They were able to do this because one of the researchers, Qiuju Wang found a family in China who had lived in the same village for centuries. Their subjects were two men whose common ancestor lived 200 years ago.
DNA is the blueprint of an organism: different species have different blueprints. And within species, individual blueprints vary. Think of the blueprint as being like an instruction manual for making the organism, a very large book with lots of chapters and pages, written in an alphabet of DNA “letters”, the nucleotides.
One such chapter is the Y chromosome, which comes down the generations through the male, virtually unchanged. It’s a very big chapter, containing some 10 million letters or nucleotides, and each one has to be compared position by position, to find the differences between two individuals.
This is what Xue and colleagues did, and they found just four mutations: four nucleotide differences (differently spelled words) amongst millions were the only differences in the DNA of the Y chromosomes of two men 13 generations apart.
Even though they had the latest DNA sequencing technology, Xue and colleagues still had to design a special strategy to search for vanishingly small number of mutations. They used “next-generation sequencing” to find the order of the “letters” on the Y chromosomes from the two men, and then compared these to a reference sequence (like a template) of the human Y chromosome.
From this they found 23 candidate single letter changes, so they amplified the regions containing them and checked them again using a method developed at Sanger. This is how they confirmed the four naturally occurring mutations. From this number, and the length of the area they searched, and the number of generations separating the individuals, they then calculated the rate of mutation.
Xue and colleagues concluded that we all carry between 100 and 200 new mutations in our DNA, equal to about one mutation in every 15 to 30 million nucleotides. Fortunately, most of these mutations are harmless and appear to have no effect on our health or appearance.
What is remarkable about this discovery is that it fits what was predicted over 70 years ago, when one of the founders of modern genetics, J B S Haldane, studied men in London with the blood disease haemophilia, and predicted that when a new individual is “made”, he or she carries about 150 new mutations across their whole DNA. Coming back to the book analogy, it’s like when a new book is made, “mistakes” creep into the new copy.
Commenting on the amount of data they crunched to find these mutations, Xue said:
“The amount of data we generated would have been unimaginable just a few years ago.”
“But finding this tiny number of mutations was more difficult than finding an ant’s egg in the emperor’s rice store,” she added.
Study coordinator Dr Chris Tyler-Smith, who is also from The Wellcome Trust Sanger Institute, said:
“These four mutations gave us the exact mutation rate – one in 30 million nucleotides each generation – that we had expected.”
“This was reassuring because the methods we used – harnessing next-generation sequencing technology – had not previously been tested for this kind of research,” explained Tyler-Smith.
New mutations are the cause of many genetic diseases, and perfecting methods that measure rates of DNA mutation reliabley means scientists can start to look more carefully at how mutation rates vary between different parts of the genomes and between individuals, he added.
“Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree.”
Yali Xue, Qiuju Wang, Quan Long, Bee Ling Ng, Harold Swerdlow, John Burton, Carl Skuce, Ruth Taylor, Zahra Abdellah, Yali Zhao, Daniel G. MacArthur, Michael A. Quail, Nigel P. Carter, Huanming Yang, Chris Tyler-Smith.
DOI:10.1016/j.cub.2009.07.032
Sources: Wellcome Trust Sanger Institute.
Written by: Catharine Paddock, PhD