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Scientists generate first complete DNA sequence of a human X chromosome

Scientists have generated the first complete DNA sequence of a human X chromosome, in a major step towards mapping the entire human genome. 

A team from the University of California and the National Human Genome Research Institute produced the first end-to-end DNA sequence as part of a new study.

Researchers say having a full sequence of the chromosome – found in human eggs and sperm – will shed fresh light on a whole host of diseases.

The results show ‘generating a human chromosome precisely’ is now possible and could lead to a fully sequenced human genome by the end of the year. 

Despite nearly two decades of improvements there are hundreds of ‘missing’ pieces of DNA that are unknown, but researchers say this discovery helps fill some gaps. 

Study authors say that by mapping this chromosome, and eventually the whole human genome, they can look for causes of different diseases and conditions.

Image depicting the puzzle pieces of DNA sequences coming together. Researchers say each piece of the chromosome DNA puzzle is harder to find than the one before it

The team behind the study said mapping different chromosomes is like trying to solve a puzzle without any unique clues or context. 

Senior author Dr Adam Phillippy said ‘imagine having to reconstruct a jigsaw puzzle’ but each tiny piece contains less context for figuring out where it comes from. 

‘The same is true for sequencing the human genome. Until now, the pieces were too small, and there was no way to put the hardest parts of the puzzle together.’ 

Gaps in the known sequences most often contain repetitive DNA segments that are exceptionally difficult to sequence. 

Yet, these repetitive segments include genes and other functional elements that may be relevant to human health and disease. 

Humans carry two sex chromosomes, the X and the Y. Women have two X chromosomes and men have an X and a Y chromosome. 

All eggs have an X chromosome – making the sperm the sole determining factor of gender, the researchers explained.


Whole genome sequencing allows researchers to read all the little bits of code that make us who we are.

The human genome is composed of more than three billion pairs of building-block molecules and grouped into some 25,000 genes.

It contains the codes and instructions that tell the body how to grow and develop, but flaws in the instructions can lead to disease.

Many argue giving patients the blood tests will allow doctors to spot rare diseases caused by genetic mutations.

Former Prime Minister David Cameron set-up a project to sequence 100,000 genomes for NHS patients with a known rare disease or cancer. 

Chief medical officer Dame Sally Davies wants to set up a central genetic database within the next five years to aid research.

She said genetic testing should become as routine as an MRI scan, although patients would have the opportunity to opt out. 

The first decoding of a human genome – completed in 2003 as part of the Human Genome Project – took 15 years and cost £2.15 billion ($3bn).  

A human genome consists of about six billion bases – too many for machines to read all at once so they are chopped into smaller pieces of a few hundred to be studied.

There are 24 human chromosomes – including X and Y – and for this new study the X chromosome was chosen due to its link to a range of illnesses.

These include conditions like haemophilia, Duchenne muscular dystrophy, cancer and autism. 

In this study, researchers did not sequence the X chromosome from a normal human cell. Instead, they used one that has two identical X chromosomes. 

Such a cell provides more DNA for sequencing than a male cell, which has only a single copy of an X chromosome. It also avoids sequence differences encountered when analysing two X chromosomes of a typical female cell.

The authors and their colleagues capitalised on new technologies that can sequence long segments of DNA. Instead of preparing and analysing small pieces of DNA. 

These large DNA molecules were then analysed by two different instruments to generate long DNA sequences that were previously impossible. 

After analysing the human X chromosome in this fashion, Phillippy and his team used their newly developed computer program to assemble the many segments of generated sequences. 

Co-senior author Dr Karen Miga, of the University of California, Santa Cruz, said: ‘We have never actually seen these sequences before in our genome, and do not have many tools to test if the predictions we are making are correct.

‘This is why it is important to have specialists in the genomics community weigh in and ensure the final product is high-quality.’

Miga’s group led the effort to close the largest remaining sequence gap on the X chromosome, the roughly 3 million bases of repetitive DNA found in the middle portion of the chromosome, called the centromere. 

The study is part of the Telomere-to-Telomere (T2T) consortium that aims to generate a complete reference sequence of the human genome in 2020.

‘We don’t yet know what we’ll find in the newly uncovered sequences,’ Phillippy said.

‘It is the exciting unknown of discovery. This is the era of complete genome sequences, and we are embracing it wholeheartedly.’ 

The results show 'generating a human chromosome precisely' is now possible and could lead to a fully sequenced human genome by the end of the year

The results show ‘generating a human chromosome precisely’ is now possible and could lead to a fully sequenced human genome by the end of the year

Potential challenges remain. Chromosomes 1 and 9, for example, have repetitive DNA segments that are much larger than the ones encountered on the X chromosome.

Dr Miga said: ‘We know these previously uncharted sites in our genome are very different among individuals, but it is important to start figuring out how these differences contribute to human biology and disease.’

Enhancing sequencing methods will continue to create new opportunities in human genetics and genomics, said the researchers.

NHGRI director Dr Eric Green said this starts a new era in genomic research.

‘The ability to generate truly complete sequences of chromosomes and genomes is a technical feat that will help us gain a comprehensive understanding of genome function and inform the use of genomic information in medical care.’

The research has been published in the journal Nature.