An international team of scientists says it has sequenced and assembled the entirety of the human genome, including parts that were missed in the sequencing of the first human genome two decades ago.
The claim, if confirmed, surpasses the achievement laid out by leaders from the Human Genome Project and Celera Genomics on the White House lawn in 2000, when they announced the sequencing of the first draft human genome. That historic draft, and subsequent human DNA sequences, have all missed about 8% of the genome.
The sequencing of the new genome fills in these gaps using new technology. It has different limitations, however, including the type of cell line that the researchers used in order to speed up their effort.
The work was detailed May 27 in a pre-print, meaning it has not yet been peer-reviewed.
Youre just trying to dig into this final unknown of the human genome, said Karen Miga, a researcher at the University of California, Santa Cruz, who co-led the international consortium that created the sequence. Its just never been done before and the reason it hasnt been done before is because its hard.
Miga emphasized that she wont consider the announcement official until the paper is peer-reviewed and published in a medical journal.
READ MORE: Psst, the human genome was never completely sequenced. Some scientists say it should be
The new genome is a leap forward, researchers say, that was made possible by new DNA sequencing technologies developed by two private sector companies: Pacific Biosciences of Menlo Park, Calif., also known as PacBio, and Oxford Nanopore, of Oxford Science Park, U.K.. Their technologies for reading out DNA have very specific advantages over the tools that have long been considered researchers gold standards.
Ewan Birney, the deputy director general of the European Molecular Biology Laboratory called the result a technical tour de force. The original genome papers were carefully worded because they did not sequence every DNA molecule from one end to the other, he noted. What this group has done is show that they can do it end-to-end. Thats important for future research, he said, because it shows what is possible.
George Church, a Harvard biologist and sequencing pioneer, called the work very important. He said he likes to note in his talks that up until now no one has sequenced the entire genome of a vertebrate something that is no longer true, if the new work is confirmed.
One important and unanswered question: How important are these missing pieces of the human puzzle? The consortium said that it increased the number of DNA bases from 2.92 billion to 3.05 billion, a 4.5% increase. But the count of protein-coding genes increased by just 0.4%, to 19,969. That doesnt mean, researchers emphasized, that the work couldnt also lead to other new insights, including those related to how genes are regulated.
The DNA sequence used was not from a person, but from a hydatidiform mole, a growth in a womans uterus caused when sperm fertilized an egg that did not have a nucleus. This meant that it contained two copies of the same 23 chromosomes, instead of two differing sets of chromosomes, as normal human cells do.
The researchers chose these cells, which had been kept in a lab, because this made the computational effort of creating the DNA sequence simpler. The original draft genome created in 2003 also contained only 23 chromosomes, but as technologies for DNA sequencing have become cheaper and simpler, researchers have tended to sequence all 46 chromosomes.
Elaine Mardis, co-executive director of the Institute for Genomic Medicine at Nationwide Childrens Hospital, worried that because these cell lines were kept in the lab, potentially mutating, the new genetic information may be largely the detritus that accumulates as a cell line is propagated over many years in culture.
Miga said that studies of the cell line had shown it to be similar to human cells, and that the researchers used cells that had been kept frozen, not propagated for many years. We went to great lengths in the preprints to demonstrate that these new sequences serve as biological reference for human genomes, Miga wrote in an email. She agreed the next step was for the group to try to sequence all 46 chromosomes, known as a diploid genome.
Why did it take 20 years for this last 8% of the genome to be sequenced, even as the cost of sequencing the rest of the genome dropped from $300 million to as little as $300? The answer has to do with the way DNA sequencing technologies work.
The current workhorse DNA sequencers, made by Illumina, take little fragments of DNA, decode them, and reassemble the resulting puzzle. This works fine for most of the genome, but not in areas where DNA code is the result of long repeating patterns. If a supercomputer only had small fragments, how could it assemble a DNA sequence that repeated AGAGAGA for bases upon bases? Thats what the missing 8% of the genome looked like.
READ MORE: At Illumina, the era of the genome has arrived. But what role will the company play?
Among these unmappable regions were one of the most recognizable structures in biology. If youve ever looked at chromosomes (think back to high school biology), they look like strings that have been knotted together. Those knots are centromeres, bundles of DNA that hold the chromosomes together. They play a key role in cell division. And they are full of repeats.
It was the centromeres, in fact, that drew Miga to want to see these missing regions.
Why are the regions that are so fundamental to life, so fundamental to how the cell operates, positioned over parts of our genome that are these giant seas of tandem repeats? she remembers asking as a grad student.
It was that question that led her, in discussion with Adam Phillippy, a researcher at the National Institutes of Health, to propose starting their current initiative, called the Telomere 2 Telomere Consortium, after the telomeres, which are the ends of the chromosome, in 2019. They signed on Evan Eichler, a University of Washington biologist who had been worried about the missing parts of the genome for years, as a co-author.
The work was possible because the Oxford Nanopore and PacBio technologies do not cut the DNA up into tiny puzzle pieces. The Oxford Nanopore technology runs a DNA molecule through a tiny hole, resulting in a very long sequence. The PacBio tech uses lasers to examine the same sequence of DNA again and again, creating a readout that can be highly accurate. Both are more expensive than the existing Illumina technology.
The companies are in a heated race. For this project, the researchers say, the PacBio technologys accuracy proved invaluable, and they used Oxford Nanopore to finish up some areas. But Oxford Nanopore has already been promising new, more usable tech. In the here and now, PacBio has the advantage but its not clear how long theyll be able to keep it, said Michael Schatz, an associate professor at Johns Hopkins University.
All the researchers spoke of a vision of the future where instead of using a single reference genome, they would assemble hundreds of different, complete genomes that are interlinked and ethnically diverse, and can be used as references. Miga is helping lead that work, as well. And this is just a step in that direction.
But until now, Schatz says, there have always been questions about what was missing. Now finally we have the right data, he said. We have the right technology.
View original post here:
Researchers may have sequenced the final unknown of the human genome - PBS NewsHour
- The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with ... - Journal of Translational... - February 18th, 2024 [February 18th, 2024]
- Polymerase Chain Reaction (PCR) - National Human Genome Research Institute - February 18th, 2024 [February 18th, 2024]
- Genomic Time Machine Reveals Secrets of Human DNA - SciTechDaily - February 18th, 2024 [February 18th, 2024]
- 1 Million Unannotated Exons Discovered in the Human Genome - Technology Networks - February 18th, 2024 [February 18th, 2024]
- Hope for the night parrot: bird's full genome has been sequenced - Cosmos - February 18th, 2024 [February 18th, 2024]
- RevIT AAV Enhancer: Rev-up AAV genome production in upstream manufacturing - BioProcess Insider - February 18th, 2024 [February 18th, 2024]
- Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced ... - Nature.com - February 18th, 2024 [February 18th, 2024]
- Secrets of Night Parrot unlocked after first genome sequenced - CSIRO - February 18th, 2024 [February 18th, 2024]
- CRISPR gene editing tool gets a revolutionary high-tech upgrade - Earth.com - February 18th, 2024 [February 18th, 2024]
- Ancient retroviruses played a key role in the evolution of vertebrate brains - EurekAlert - February 18th, 2024 [February 18th, 2024]
- Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application - Nature.com - February 18th, 2024 [February 18th, 2024]
- Hopes elusive parrots genome will provide answers - news.com.au - February 18th, 2024 [February 18th, 2024]
- MicroRNA is the master regulator of the genome researchers are learning how to treat disease by harnessing the ... - The Conversation - November 30th, 2023 [November 30th, 2023]
- "Ground-Breaking" Release of World's Largest Whole Genome Resource - Inside Precision Medicine - November 30th, 2023 [November 30th, 2023]
- Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet - Nature.com - November 30th, 2023 [November 30th, 2023]
- Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China - Virology Journal - Virology Journal - November 30th, 2023 [November 30th, 2023]
- Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- CRISPR-Based "Genome Shredding" Technique Shows Promise in Treating Glioblastoma - Inside Precision Medicine - November 30th, 2023 [November 30th, 2023]
- Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- TRISH to investigate the effects of spaceflight on the human genome, central nervous system - Odessa American - November 30th, 2023 [November 30th, 2023]
- The venom preceded the stinger: Genomic studies shed light on the origins of bee venom - EurekAlert - November 30th, 2023 [November 30th, 2023]
- Integrating genomic and multiomic data for Angelica sinensis provides insights into the evolution and biosynthesis of ... - Nature.com - November 30th, 2023 [November 30th, 2023]
- Genetic diversity and ancestry of the Khmuic-speaking ethnic groups ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Researchers to Apply Genome Analysis to Childhood Cancers; Goal ... - The Japan News - September 21st, 2023 [September 21st, 2023]
- How Bats' Genomes May Help Them Avoid Cancer and Survive ... - Technology Networks - September 21st, 2023 [September 21st, 2023]
- Longitudinal genomic surveillance of carriage and transmission of ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Whole genomes from bacteria collected at diagnostic units around ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Genome-wide identification of lncRNA & mRNA for T2DM | PGPM - Dove Medical Press - September 21st, 2023 [September 21st, 2023]
- Tasmanian tiger RNA is first to be recovered from an extinct animal - Nature.com - September 21st, 2023 [September 21st, 2023]
- Loneliness and depression: bidirectional mendelian randomization ... - Nature.com - September 21st, 2023 [September 21st, 2023]
- Rome Therapeutics adds $72 million to Series B round to harness ... - OutSourcing-Pharma.com - September 21st, 2023 [September 21st, 2023]
- Mystery of 'living fossil' tree frozen in time for 66 million years finally ... - Livescience.com - September 21st, 2023 [September 21st, 2023]
- Why the human genome could be healthcares holy grail - Yahoo Finance - May 4th, 2023 [May 4th, 2023]
- Scientists Compare Genomes of 240 Mammals to Understand Human DNA - The New York Times - May 4th, 2023 [May 4th, 2023]
- Genomes From 240 Mammalian Species Help Explain 100 Years Of Evolution And Human Disease - ABP Live - May 4th, 2023 [May 4th, 2023]
- 'Deletions' from the human genome may be what made us human - Yale News - May 4th, 2023 [May 4th, 2023]
- GeneDx Adds Buccal Swab as Non-Invasive Whole Genome ... - GlobeNewswire - May 4th, 2023 [May 4th, 2023]
- Whole-genome sequencing used to track down genes behind familial glioma - Medical Xpress - May 4th, 2023 [May 4th, 2023]
- Wiggly proteins guard the genome: Dynamic network in the pores of ... - Science Daily - May 4th, 2023 [May 4th, 2023]
- Genome-Wide Splicing Quantitative Expression Locus Analysis ... - Cancer Discovery - May 4th, 2023 [May 4th, 2023]
- Digital Genome Market is expand at a CAGR of 8.6% to reach USD ... - Digital Journal - May 4th, 2023 [May 4th, 2023]
- High School Students Learn the Basics of Base Editing to Cure GFP ... - University of California San Diego - May 4th, 2023 [May 4th, 2023]
- Genomic researchers gain access to CSIRO's AI-powered data ... - Microsoft - May 4th, 2023 [May 4th, 2023]
- Archaic hominin traits through the splicing lens - Nature.com - May 4th, 2023 [May 4th, 2023]
- Critical bug in genome sequencing device scores '10' on CVSS ratings - SC Media - May 4th, 2023 [May 4th, 2023]
- Novel Genomic Approach Ensures Better Diagnosis of Hereditary ... - Technology Networks - May 4th, 2023 [May 4th, 2023]
- Intellia Therapeutics: Leading the Way in Revolutionary Genome ... - Best Stocks - May 4th, 2023 [May 4th, 2023]
- Visual tracking of viral infection dynamics reveals the synergistic ... - Nature.com - May 4th, 2023 [May 4th, 2023]
- Genome | Genome LLC | United States - March 31st, 2023 [March 31st, 2023]
- Belarus: EU and WHO deliver equipment for research of genomes of infectious disease agents - EIN News - February 24th, 2023 [February 24th, 2023]
- Gene vs. genome: Definition, function, and impact - January 30th, 2023 [January 30th, 2023]
- Big cog in the wheel: As Covid worries reappear, Insacogs genome sequencing ability must be aided by govts - Times of India - December 25th, 2022 [December 25th, 2022]
- CapitalGainsReport Sector Spotlight: Healthcare Penny Stocks On The Move (ARDX, WHSI, BNGO) - Marketscreener.com - November 25th, 2022 [November 25th, 2022]
- Genome Insight and Kun-hee Lee Child Cancer & Rare Disease Project Team of SNUH (Seoul National University Hospital) Made an Agreement About a... - November 23rd, 2022 [November 23rd, 2022]
- Genome-wide association study reveals distinct genetic associations related to leaf hair density in two lineages of wheat-wild relative Aegilops... - October 19th, 2022 [October 19th, 2022]
- The Global Genomics Market to Exhibit Growth at a CAGR of 16.90% During the Forecast Period (20222027) | DelveInsight - Yahoo Finance - October 19th, 2022 [October 19th, 2022]
- Illumina and GenoScreen Partner to Expand Access to Genomic Testing for Multidrug-Resistant Tuberculosis - PR Newswire - October 19th, 2022 [October 19th, 2022]
- Superresolution Method Poised to Better Gene Function Understanding - Photonics.com - October 19th, 2022 [October 19th, 2022]
- Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians - Nature.com - October 15th, 2022 [October 15th, 2022]
- How a New Battery Data Genome Project Will Use Vast Amounts of Information to Build Better EVs - InsideClimate News - October 15th, 2022 [October 15th, 2022]
- Scientists Reconstruct the Genome of the 180-Million-Year-Old Common Ancestor of All Mammals - SciTechDaily - October 15th, 2022 [October 15th, 2022]
- Combining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic... - October 15th, 2022 [October 15th, 2022]
- Concerted expansion and contraction of immune receptor gene repertoires in plant genomes - Nature.com - October 15th, 2022 [October 15th, 2022]
- Uncovering the Full Variant Continuum with Pioneering Solutions from Bionano - Inside Precision Medicine - October 15th, 2022 [October 15th, 2022]
- Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau | Scientific Reports - Nature.com - October 15th, 2022 [October 15th, 2022]
- Research Assistant in Molecular and Genome Editing Therapeutics job with KINGS COLLEGE LONDON | 311876 - Times Higher Education - October 15th, 2022 [October 15th, 2022]
- Lessons learnt from COVID-19 shed light on future pandemic preparedness - The Peter Doherty Institute for Infection and Immunity - October 15th, 2022 [October 15th, 2022]
- From Neanderthal genome to Nobel prize: meet geneticist Svante Pbo - Nature.com - October 8th, 2022 [October 8th, 2022]
- Revealing the genome organization of the earliest common ancestor of all mammals - Tech Explorist - October 8th, 2022 [October 8th, 2022]
- Mitochondrial DNA Is Working Its Way Into the Human Genome - Technology Networks - October 8th, 2022 [October 8th, 2022]
- Animated Map: Where to Find Water on Mars - Visual Capitalist - October 8th, 2022 [October 8th, 2022]
- Reconstruction of The First Mammal's Genome Suggests It Had 38 Chromosomes - ScienceAlert - October 6th, 2022 [October 6th, 2022]
- Genomic Science Breakthroughs Are Happening Faster Than Ever Thanks to HPC - CIO - October 6th, 2022 [October 6th, 2022]
- Genome Of Ancient Humans Is The Winning Field Of 2022's Nobel Prize in Medicine - IFLScience - October 6th, 2022 [October 6th, 2022]
- ASU professor to study new genome editing tools with NIH Innovator Award - ASU News Now - October 6th, 2022 [October 6th, 2022]
- New R&D norms to fast-track research on genome-edited crops - The Financial Express - October 6th, 2022 [October 6th, 2022]