July 4, 2022

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The human genome is finally COMPLETE

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The human genome has finally been completely mapped, 20 years after the first draft was produced, scientists have revealed.

Today, researchers have published a gap-free sequence of roughly 3 billion bases (or ‘letters’) an a single person’s DNA.

According to team, a complete, gap-free sequence of bases in our DNA is critical for understanding human genomic variation and genetic contributions to certain diseases.

In addition to the medical implications, the full genome helps to answer the question of what makes us distinctly human.

Some of the genes that were gaps in the original genome are thought to be critically important in helping to make a bigger brain in humans compared to other apes, the researchers suggest. 

The $3 billion Human Genome Project, which was completed in April 2003, mapped around 92 per cent of the genome. Researchers now claim to have mapped the remaining 8 per cent

WHAT IS A GENOME? 

Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA. All living things – plants, bacteria, viruses and animals – have a genome.

Your genome is all 3.2 billion letters of your DNA. It contains around 20,000 genes.

Genes are the instructions for making the proteins our bodies are built of – from the keratin in hair and fingernails to the antibody proteins that fight infection. 

Source: Genomics England 

The work was done by the Telomere to Telomere (T2T) consortium, which included researchers at the National Human Genome Research Institute (NHGRI); the University of California, Santa Cruz (UCSC); and University of Washington, Seattle.  

The newly completed genome, dubbed T2T-CHM13, is now accessible through the online UCSC Genome Browser.  

‘Generating a truly complete human genome sequence represents an incredible scientific achievement, providing the first comprehensive view of our DNA blueprint,’ said Eric Green, director of NHGRI in Bethesda, Maryland. 

‘This foundational information will strengthen the many ongoing efforts to understand all the functional nuances of the human genome, which in turn will empower genetic studies of human disease.’ 

T2T-CHM13 represents a major upgrade from the current reference genome, called GRCh38, which is used by doctors when searching for mutations linked to disease, as well as by scientists looking at the evolution of human genetic variation.  

The achievement comes two decades after the Human Genome Project produced the first draft human genome sequence. 

The $3 billion Human Genome Project, which was completed in April 2003, mapped around 92 per cent of the genome. 

GENES, GENOMES AND DNA 

Gene: a short section of DNA

Chromosome: a package of genes and other bits of DNA and proteins

Genome: an organism’s complete set of DNA

DNA: Deoxyribonucleic acid – a long molecule that contains unique genetic code 

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Your genome is the instructions for making and maintaining you. It is written in a chemical code called DNA. All living things – plants, bacteria, viruses and animals – have a genome.

Your genome is all 3.2 billion letters of your DNA. It contains around 20,000 genes.

Genes are the instructions for making the proteins our bodies are built of – from the keratin in hair and fingernails to the antibody proteins that fight infection. 

Source: Genomics England/Your Genome/Cancer Research

Crucial regions accounting for the remaining 8 per cent stayed hidden from scientists for more than two decades because they did not have the technology.

But developments have made filling in the gaps possible, and have helped to reveal parts of the genome that had evaded scientists.

In other words, they’ve added a whole chromosome’s worth of previously hidden DNA ­– the missing eight per cent.  

‘These parts of the human genome that we haven’t been able to study for 20-plus years are important to our understanding of how the genome works, genetic diseases, and human diversity and evolution,’ said Karen Miga of the University of California, Santa Cruz, who organised the T2T consortium. 

According to consortium co-chairman Adam Phillippy, sequencing a person’s entire genome should get less expensive and more straightforward in the coming years.

‘In the future, when someone has their genome sequenced, we will be able to identify all of the variants in their DNA and use that information to better guide their healthcare,’ he said.  

‘Truly finishing the human genome sequence was like putting on a new pair of glasses.

‘Now that we can clearly see everything, we are one step closer to understanding what it all means.’  

A genome is the complete set of genetic information in an organism, stored in long molecules of DNA called chromosomes. 

DNA, or deoxyribonucleic acid, is a complex chemical in almost all organisms that carries genetic information. 

DNA is made up of four building blocks called nucleotides, each denoted by a letter. They are adenine (A), thymine (T), guanine (G), and cytosine (C). 

DNA is made up of four building blocks called nucleotides – adenine (A), thymine (T), guanine (G), and cytosine (C)

DNA is made up of four building blocks called nucleotides – adenine (A), thymine (T), guanine (G), and cytosine (C)

T2T-CHM13 COULD EXPLAIN ‘RAPID’ HUMAN EVOLUTION

The T2T results also point to more complex patterns of variation in genes that may have helped create the human species – and could explain our rapid evolution.

The full genome sequence reveals that some genes associated with bigger brains are highly variable. 

One person might have 10 copies of a particular gene, while others might have only one or two. 

This variation can spell trouble during fertilization, when chromosomes from mom and dad line up and swap pieces.

The mismatched genes can lead to ‘an earthquake’ of gene alterations, said Evan Eichler, researcher at the University of Washington School of Medicine and T2T consortium co-chair.

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As a result, ‘these regions become a crucible for both rapid evolutionary changes and disease susceptibility, both within and between species,’ he said. 

The human genome is made up of just over six billion individual letters of DNA – about the same number as other primates like chimps – spread among 23 pairs of chromosomes. 

To read a genome, scientists first chop up all that DNA into pieces hundreds to thousands of letters long. 

Sequencing machines then read the individual letters in each piece, and scientists try to assemble the pieces in the right order, like putting together an intricate puzzle.

One challenge is that some regions of the genome repeat the same letters over and over again. 

Repetitive regions include the centromeres, the parts that hold the two strands of chromosomes together and that play crucial roles in cell division, and ribosomal DNA, which provides instructions for the cell’s protein factories.  

Another issue is that most cells contain two genomes ­– one from the father and one from the mother. 

When researchers try to assemble all the pieces, sequences from each parent can mix together, obscuring the actual variation within each individual genome.

In the mid-2000s, as scientists tried to figure out how to overcome the barriers, they came up with the idea of getting a complete genome by sequencing just one of the genomes instead of solving two at the same time.

They used a set of cell lines – population of cells that can be maintained in culture for an extended period of time – that were being studied by University of Pittsburgh reproductive geneticist Urvashi Surti. 

Karen Miga, assistant professor of biomolecular engineering at UC Santa Cruz, co-founded the Telomere-to-Telomere (T2T) consortium to pursue a complete, gapless assembly of a human genome sequence

Karen Miga, assistant professor of biomolecular engineering at UC Santa Cruz, co-founded the Telomere-to-Telomere (T2T) consortium to pursue a complete, gapless assembly of a human genome sequence

Repetitive regions of the genome include the centromeres, the parts that hold the two strands of chromosomes together and that play crucial roles in cell division. The spindles (green) that pull chromosomes apart during cell division are attached to a protein complex called the kinetochore, which latches onto the chromosome at a place called the centromere - a region containing highly repetitive DNA sequences

Repetitive regions of the genome include the centromeres, the parts that hold the two strands of chromosomes together and that play crucial roles in cell division. The spindles (green) that pull chromosomes apart during cell division are attached to a protein complex called the kinetochore, which latches onto the chromosome at a place called the centromere – a region containing highly repetitive DNA sequences

Because of a rare glitch in normal development, the cells used had two copies of the father’s DNA and none of the mother’s.

Such a cell line, with only one genome, is what made this genome assembly possible.

Another key aspect of the research was the ability of new machines to accurately read a million letters of DNA, which opened the door to finally tackling the genome’s ‘hard bits’. 

Over the past decade, two new DNA sequencing technologies emerged that produced much longer sequence reads. 

The Oxford Nanopore DNA sequencing method can read up to 1 million DNA letters in a single read with modest accuracy, while the PacBio HiFi DNA sequencing method can read about 20,000 letters with nearly perfect accuracy. 

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Researchers in the T2T consortium used both DNA sequencing methods to generate the complete human genome sequence.  

An organism's genome is written in a chemical code called DNA. DNA, or deoxyribonucleic acid, is a complex chemical in almost all organisms that carries genetic information. Pictured, artistic 3D rendering of a DNA double helix

An organism’s genome is written in a chemical code called DNA. DNA, or deoxyribonucleic acid, is a complex chemical in almost all organisms that carries genetic information. Pictured, artistic 3D rendering of a DNA double helix

The sequence will be particularly valuable for studies that aim to establish comprehensive views of human genomic variation, or how people’s DNA differs. 

Such insights are vital for understanding the genetic contributions to certain diseases and for using genome sequence as a routine part of clinical care in the future. 

Many research groups have already started using a pre-release version of the complete human genome sequence for their research. 

‘Ever since we had the first draft human genome sequence, determining the exact sequence of complex genomic regions has been challenging,’ said Evan Eichler, researcher at the University of Washington School of Medicine and T2T consortium co-chair.

‘I am thrilled that we got the job done. The complete blueprint is going to revolutionise the way we think about human genomic variation, disease and evolution.’

Six papers encompassing the completed sequence appear in Science, along with companion papers in several other journals.  

DNA: A COMPLEX CHEMICAL THAT CARRIES GENETIC INFORMATION IN ALMOST ALL ORGANISMS

DNA, or deoxyribonucleic acid, is a complex chemical in almost all organisms that carries genetic information.

It is located in chromosomes the cell nucleus and almost every cell in a person’s body has the same DNA. 

It is composed of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T).

The structure of the double-helix DNA comes from adenine binding with thymine and cytosine binding with guanine. 

Human DNA consists of three billion bases and more than 99 per cent of those are the same in all people.

The order of the bases determines what information is available for maintaining an organism (similar to the way in which letters of the alphabet form sentences).

The DNA bases pair up with each other and also attach to a sugar molecule and phosphate molecule, combining to form a nucleotide.

These nucleotides are arranged in two long strands that form a spiral called a double helix.

The double helix looks like a ladder with the base pairs forming the rungs and the sugar and phosphate molecules forming vertical sidepieces.

A new form of DNA was recently discovered inside living human cells for the first time.

Named i-motif, the form looks like a twisted ‘knot’ of DNA rather than the well-known double helix. 

It is unclear what the function of the i-motif is, but experts believe it could be for ‘reading’ DNA sequences and converting them into useful substances.

Source: US National Library of Medicine

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