First Individual Genome Sequence Published Sequence Reveals That Human-To-Human Variation Is Substantially Greater Than Earlier Estimates

Independent sequence and assembly of the six billion base pairs from the
genome of one person ushers in the era of individualized genomics.




Researchers at the J. Craig Venter Institute (JCVI), along with
collaborators at The Hospital for Sick Children in Toronto and the
University of
California San Diego (UCSD), have published a genome sequence of an
individual, Craig Venter, that covers both sets of chromosomes that were
inherited
from each parent.



Two other versions of the human genome currently exist-one published in
2001 by J. Craig Venter, Ph.D., and colleagues at Celera Genomics, and
another at the same time by a consortium of government-funded researchers.
These genomes were not of any single individual, but, rather, were a
melding of DNA from various people. In the case of Celera, it was a
consensus assembly from five individuals, while the government-funded
version was
a haploid genome based on sequencing from a limited number of individuals.
Both versions greatly underestimated human genetic diversity.



This new genome, known as the "HuRef" version, represents the first time a
true diploid genome from one individual - Dr. Venter- has been
published. The research is available in the latest issue of the
open-access journal PLoS Biology.



Researchers at the JCVI have been sequencing and analyzing this version of
Dr. Venter's genome since 2003. Building on reanalyzed data from Dr.
Venter's genome that constituted 60% of the previously published Celera
genome, the team had the goal of constructing a true reference human
genome
based on one individual. Using whole genome shotgun sequencing and highly
accurate long reads from Sanger dideoxy automated DNA sequencing, the team
produced additional data making the final 32 million sequences.



From the combined data set of more than 20 billion base pairs, the
researchers were able to assemble the human genome with an overall length
of 2.810
billion base pairs. The genome was covered 7.5 times, ensuring that each
set of contributing chromosomes was covered over 3.2 times for greater
than
96% coverage of the two parental genomes. The team at JCVI compared and
contrasted the new HuRef diploid genome sequence to earlier versions of
published human genomes and found that the HuRef version improved upon
both these early versions by providing more and correctly oriented base
pairs.




Since the HuRef genome is diploid, each of the parental chromosomes could
be directly compared to each other. One of the most surprising and
important
findings from this research was the high degree of genetic variation that
was found between two chromosomes within a single individual.



"Each time we peer into the human genome, we uncover more valuable insight
into our intricate biology," said Dr. Venter. "With this publication,
we have shown that human-to-human variation is more than seven-fold
greater than earlier estimates, proving that we are in fact very unique
individuals at the genetic level." He added, "It is clear, however, that
we are still at the earliest stages of discovery about ourselves, and
only with continued sequencing of more individual genomes will we be able
to garner a full understanding of how our genes influence our lives."
















Within the human genome, there are different kinds of DNA variants. The
most studied type is single nucleotide polymorphisms, or SNPs. These have
long
been thought to be the most prevalent and perhaps the most important type
of variant implicated in human traits and disease susceptibility. However,
in this analysis of Dr. Venter's genome, the team found a surprising
number of other important variants. A total of 4.1 million variants
covering
12.3 million base pairs of DNA were uncovered with more than 1.2 million
new variants discovered.



Of the 4.1 million variations between chromosome sets, 3.2 million were
SNPs, while nearly one million were other kinds of variants, such as
insertion/deletions ("indels"), copy number variants, block substitutions,
and segmental duplications. While the SNPs outnumbered the non-SNP
types of variants, the non-SNP variants involved a larger portion of the
genome. This suggests that human-to-human variation is much greater than
previously thought. The researchers suggest that much more research needs
to be done on these non-SNP variants to better understand their role in
individual genomics.



According to Sam Levy, Ph.D., lead author and senior scientist at JCVI,
"The ability to use unbiased, high throughput sequencing methods, coupled
with advance computational analytic methods, enables us to characterize
more comprehensively the wide variety of individual genetic variation.
This
offers us an unprecedented opportunity to study the prevalence and impact
of these DNA variants on traits and diseases in human populations."



Another important feature that is made possible by having an individual,
diploid genome is the ability to begin to do better and more informed
haplotype assemblies. Haplotypes are groups of linked variants. Through
the government-sponsored HapMap project, many common haplotypes have been
identified; however, these are based on averages of large ethnogeographic
populations rather than individuals. Having individual haplotypes would
enable researchers to understand and find more rare or individual variants
that would explain and help predict diseases in that particular person-a
truly personalized, individualized genomics paradigm. In the HuRef
analysis, the team used the 4.1 million variant set and new algorithms to
build
haplotype assemblies that, when compared to the HapMap project,
represented longer and more complete linkages. The JCVI researchers expect
this number
to improve significantly as additional sequence coverage is added to HuRef
using a variety of new sequencing technologies.



Long-range haplotype linkages will enable much more complete analysis of
human variation and the genetic association with complex human traits,
behaviors, and diseases. In the near future, the scientists believe that
it will be possible to know from which parent various traits were
inherited.


Already in this analysis, the JCVI team has found more than 300 disease
genes and 4,000 genes overall that exhibit different protein forms. This
will
be an important area for further study and analysis to determine how these
altered proteins affect Dr. Venter's health status.



Citation: Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The
diploid genome sequence of an individual human. PLoS Biol 5(10): e254.
doi:10.1371/journal.pbio.0050254.

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