Studeo
11th June 2010, 21:04
Source: BioTechniques
http://www.biotechniques.com/news/More-than-2000-genes-missing-in-the-human-reference-genome/biotechniques-296801.html
More than 2000 sequences missing in the human reference genome
06/08/2010
Uduak Grace Thomas
Researchers have discovered more than 2000 DNA sequences that aren’t in the human genome reference map.
A research team at the University of Washington (UW) has discovered more than 2000 DNA sequences that aren’t in the reference human genome reference map. Next-generation sequencing techniques rely upon this reference map to align the small fragments that they decode, and the missing sequences could contain important information about genetic disease.
The UW team inserted the DNA fragments from nine donors into bacteria and then mapped the sequences to the human reference genome. When they analyzed their results, they discovered 2363 sequences weren’t on the map.
“A large portion of those sequences are either missing, fragmented, or misaligned when compared to results from next-generation sequencing genome assemblies on the same samples,” said Evan Eichler, a genomic science professor at UW, Howard Hughes Medical Investigator, and senior author of the paper, in a press release.
The team says that the sequences could have been excluded during the creation of the reference map, or misaligned, since individuals can have varying numbers of copies of particular sequences. “When the human genome was put together, at any given position, its essentially one haplotype that’s represented there,” Eichler told BioTechniques. “So [what] follows from that [is] that there must be pieces of DNA that we know nothing about that exist in maybe the majority of humans.”
When Eichler’s team aligned their sequences against other non-reference human genomes, they discovered that the frequency of certain sequences changed between different geographic populations. If a donor to a particular section of the reference map came from a part of the world where a particular sequence was not conserved, then the sequence would have been excluded from the map.
Eichler and his colleagues plan to use their technique to create a more complete picture of the human genome. “I imagine that what will come out of this [is] a more comprehensive view of how dynamic our genome is and how that relates to human health,” he said.
The paper “Characterization of missing human genome sequences and copy-number polymorphic insertions,” was published in online ahead of print in the Apr. 18 edition of Nature Methods.
http://www.biotechniques.com/news/More-than-2000-genes-missing-in-the-human-reference-genome/biotechniques-296801.html
More than 2000 sequences missing in the human reference genome
06/08/2010
Uduak Grace Thomas
Researchers have discovered more than 2000 DNA sequences that aren’t in the human genome reference map.
A research team at the University of Washington (UW) has discovered more than 2000 DNA sequences that aren’t in the reference human genome reference map. Next-generation sequencing techniques rely upon this reference map to align the small fragments that they decode, and the missing sequences could contain important information about genetic disease.
The UW team inserted the DNA fragments from nine donors into bacteria and then mapped the sequences to the human reference genome. When they analyzed their results, they discovered 2363 sequences weren’t on the map.
“A large portion of those sequences are either missing, fragmented, or misaligned when compared to results from next-generation sequencing genome assemblies on the same samples,” said Evan Eichler, a genomic science professor at UW, Howard Hughes Medical Investigator, and senior author of the paper, in a press release.
The team says that the sequences could have been excluded during the creation of the reference map, or misaligned, since individuals can have varying numbers of copies of particular sequences. “When the human genome was put together, at any given position, its essentially one haplotype that’s represented there,” Eichler told BioTechniques. “So [what] follows from that [is] that there must be pieces of DNA that we know nothing about that exist in maybe the majority of humans.”
When Eichler’s team aligned their sequences against other non-reference human genomes, they discovered that the frequency of certain sequences changed between different geographic populations. If a donor to a particular section of the reference map came from a part of the world where a particular sequence was not conserved, then the sequence would have been excluded from the map.
Eichler and his colleagues plan to use their technique to create a more complete picture of the human genome. “I imagine that what will come out of this [is] a more comprehensive view of how dynamic our genome is and how that relates to human health,” he said.
The paper “Characterization of missing human genome sequences and copy-number polymorphic insertions,” was published in online ahead of print in the Apr. 18 edition of Nature Methods.