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Human X chromosome sequenced for the fist time, from telomere to telomere

dna sequencing genome assembly algorithms genome informatics

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#1 Engadin

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Posted 15 July 2020 - 09:47 PM


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S O U R C E :   New Atlas

 

P A Y W A L L E D   P R I M A L    S O U R C E :   nature (Telomere-to-telomere assembly of a complete human X chromosome)

 

 

 

 

 

 

depositphotos-177206294-l-2015.jpg

 

The human X chromosome has been completely sequenced from end to end for the first time. Giovanni_Cancemi/Depositphotos

 

 

 

As close as we’ve gotten to sequencing the entire human genome, there are still a few gaps. But now geneticists have plugged a major one in a landmark new study, by sequencing the entire human X chromosome from end to end, covering more than three million base pairs that were previously unmapped.

 
The Human Genome Project was one of the most ambitious scientific undertakings of all time. Between 1990 and 2003, an international team of scientists worked to sequence the human genome in high detail, with the end result being an almost complete blueprint for the human species.
 
But the emphasis there is on “almost.” The first version covered a little over 92 percent of the human genome, with more than 99.99 percent accuracy. Later revisions closed some of the gaps, but others still remain.
 
The biggest gaps were located at the center and ends of chromosomes, which are known as centromeres and telomeres respectively. These regions are categorized by huge sections of repeating sequences, which can be hard to sort out.
 
Now an international team of geneticists has patched these gaps up. The researchers managed to sequence the entire X chromosome for the first time, from telomere to telomere.
 
In humans, the X chromosome is one of the sex-determining chromosomes passed down from parent to child. Generally, a zygote that receives two X chromosomes – one from each parent – will be usually biologically female, while an X and a Y chromosome results in a male.
 
In this case, the team didn’t sequence an X chromosome from a normal human cell. Instead, they studied a special type of cell that contains two identical chromosomes, part of a model genome dubbed CHM13.
 
One problem with sequencing genomes is that the technology traditionally can only read short segments of DNA at a time, leaving scientists to piece it all together. Unfortunately, that can be particularly difficult when those segments repeat over and over, which the team likens to assembling a jigsaw puzzle that’s all one color.
 
To finish the puzzle, the team used new techniques that read much longer sequences at a time. One of these is what’s known as “nanopore technology,” which funnels single molecules of DNA through a tiny hole and sequences them by detecting changes in the current flow.
 
“These repeat-rich sequences were once deemed intractable, but now we’ve made leaps and bounds in sequencing technology,” says Karen Miga, lead researcher on the project. “With nanopore sequencing, we get ultra-long reads of hundreds of thousands of base pairs that can span an entire repeat region, so that bypasses some of the challenges.”

 







Also tagged with one or more of these keywords: dna sequencing, genome assembly algorithms, genome informatics

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