Sequencing the Human Genome

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The human genome is the complete set of genetic information, stored as DNA within the nucleus of nearly every one of the trillions of cells in the human body. Every person’s genome is different and is a large part of what makes us into unique individuals. The first effort to decode the human genome, considered a draft sequence, resulted in its publication in 2001. Six years later a high quality sequence—called a diploid genome—of a single individual was published, containing all genetic information from both parents.

The future of genomic research

In the 20 years since the draft sequence publication, genomic sequencing has become common in social discourse around the world. Further advancements in technology have significantly decreased the cost and time it takes to sequence an individual genome. The first draft human genome took 9 months and $100 million to complete. Today a human genome can be sequenced for less than $1000 and takes only a few hours. The sequencing technology used in 2001 took up an entire warehouse. Today the smallest sequencers can be held in the palm of your hand. As a result, millions of genomes have been sequenced and interpreted, at least to some level, leading to advancements in our understanding of human health and genomics. Even with these milestones behind us, we are still just scratching at the surface. Today, researchers at the J. Craig Venter Institute continue on the quest for a new and better understanding of human genomics.

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The first draft human genome

Decoding the human genome was a monumental scientific undertaking, requiring the development of new tools and techniques, including significant advancements in sequencing and computational technology.

In the 1990s, Dr. Venter and his team at the US National Institutes of Health developed Expressed Sequence Tags or ESTs, allowing for the rapid discovery of new genes. Later in 1995, after founding The Institute of Genomic Research (TIGR), Venter and team developed whole shotgun sequencing to decipher the DNA sequence of the first free-living organism, the bacterium Haemophilus influenzae. Both of these techniques would prove to be instrumental in the challenges ahead.

Armed with the latest sequencing technology developed by Applied Biosystems, Venter co-founded Celera Genomics in 1998, a commercial company embarking on the landmark scientific quest to sequence and analyze the human genome. Two years after sequencing the model organism the fruit fly as a test project, President Bill Clinton announced the completion of the first draft human genome at a White House press conference, proclaiming it to be “the most wonderous map ever produced by humankind.” The findings were published in the February 2001 edition of the journal Science in conjunction with the federally-funded US and international human genome project published in Nature.

The first draft human genome comprised DNA from five individuals, totaling 14.8 billion base pairs. It took nine months and 27,271,853 high-quality sequence reads to generate. It was a monumental first step toward improving our understanding of human health, genetic drivers of disease, and the interplay between the environment and genetics.

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The first publication of a diploid human genome from one person: A step closer to truly individualized genomic medicine

Originally, two versions of the human genome were published enabling researchers a first look at humans at our most basic level. While these achievements marked a new era in science, it was clear that more analysis and more sequenced genomes were needed for a more complete understanding of human biology. And because these first published genomes were mosaics of many people's genomes, rather than the genome of one individual, it was likely that much of the key information about each person, such as what particular traits or propensity for disease were coded for in their genes, was missing. In short, the era of true individualized genomic medicine was not yet realized.

In 2007, researchers at the J. Craig Venter Institute, along with collaborators from Hospital for Sick Children in Toronto, the University of California, San Diego, and the Universidad de Barcelona in Spain published the first diploid genome of an individual, Dr. Venter, in PLoS Biology. This analysis and assembly of the 20 billion base pairs of Dr. Venter’s DNA was the first look at both sets of an individual’s chromosomes, one inherited from each of his parents. The resulting sequence showed that genetic variation between individuals is five to seven times greater than previously observed in human-to-human genome comparison.

The data from the human diploid genome was made available through the public repository at NCBI at the time of publication. JCVI researchers also developed an open-source genome browser that highlighted the newly discovered variation.

This new individual genome had tantalizing vistas: more than 4.1 million genetic variants covering 12.3 million base pairs of DNA; more than 3.2 million single nucleotide polymorphisms (SNPs); 1.2 million never before seen variants; and nearly a million non-SNP variants. It served as the baseline reference for human genomic research moving forward.
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Videos

Draft of the Human Genome Sequence Announcement at the White House (2000)
How DNA Sequencing Works — Human Diploid Genome Project (HuRef)
First Diploid Genome of an Individual — Human Diploid Genome Project (HuRef)

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Publications

Mobile elements create structural variation: analysis of a complete human genome.
Genome research. 2009-09-01; 19.9: 1516-26.
PMID: 19439515
The HuRef Browser: a web resource for individual human genomics.
Nucleic acids research. 2009-01-01; 37.Database issue: D1018-24.
PMID: 19036787
A new human genome sequence paves the way for individualized genomics.
PLoS biology. 2007-10-01; 5.10: e266.
PMID: 20076646
On the sequencing and assembly of the human genome.
Proceedings of the National Academy of Sciences of the United States of America. 2002-04-02; 99.7: 4145-6.
PMID: 11904395
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X
The sequence of the human genome.
Science (New York, N.Y.). 2001-02-16; 291.5507: 1304-51.
PMID: 11181995

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