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Thousands of never-before-seen human genome variations uncovered

Date: November 10, 2014

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Source: University of Washington Health Sciences/UW Medicine

Summary: Thousands of never-before-seen genetic variants in the human genome
have been uncovered using a new genome sequencing technology.
These discoveries close many human genome mapping gaps that have
long resisted sequencing. The technique, called single-molecule, realtime DNA sequencing, may now make it possible for researchers to
identify potential genetic mutations behind many conditions whose
genetic causes have long eluded scientists.

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Related Topics
Health & Medicine
Genes
Human Biology

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DNA (stock illustration). Researchers are exploring the use of new technologies for
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[Click to enlarge image]

housands of never-before-seen genetic variants in the human genome

have been uncovered using a new genome sequencing technology.
These discoveries close many human genome mapping gaps that
have long resisted sequencing.
The technique, called single-molecule, real-time DNA
sequencing (SMRT), may now make it possible for
researchers to identify potential genetic mutations
behind many conditions whose genetic causes have
long eluded scientists, said Evan Eichler, professor of
genome sciences at the University of Washington, who
led the team that conducted the study.

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"We now have access to a whole new realm of genetic

variation that was opaque to us before," Eichler said.

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Eichler and his colleague report their findings Nov. 10 in

the journal Nature.
To date, scientists have been able to identify the genetic causes of only about half of

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inherited conditions. This puzzle has been called the "missing heritability problem."
One reason for this problem may be that standard genome sequencing technologies
cannot map many parts of the genome precisely. These approaches map genomes by
aligning hundreds of millions of small, overlapping snippets of DNA, typically about 100
bases long, and then analyzing their DNA sequences to construct a map of the
genome.
This approach has successfully pinpointed millions of small variations in the human
genome. These variations arise from substitution of a single nucleotide base, called a
single-nucleotide polymorphisms or SNP. The standard approach also made it
possible to identify very large variations, typically involving segments of DNA that are
5,000 bases long or longer. But for technical reasons, scientists had previously not
been able to reliably detect variations whose lengths are in between -- those ranging
from about 50 to 5,000 bases in length.
The SMRT technology used in the new study makes it possible to sequence and read
DNA segments longer than 5,000 bases, far longer than standard gene sequencing
technology.
This "long-read" technique, developed by Pacific Biosciences of California, Inc. of
Menlo Park, Calif., allowed the researchers to create a much higher resolution
structural variation map of the genome than has previously been achieved. Mark
Chaisson, a postdoctoral fellow in Eichler's lab and lead author on the study,
developed the method that made it possible to detect structural variants at the base
pair resolution using this data.

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To simplify their analysis, the researchers used the genome from a hydatidiform mole,
an abnormal growth caused when a sperm fertilizes an egg that lacks the DNA from
the mother. The fact that mole genome contains only one copy of each gene, instead
of the two copies that exist in a normal cell. simplifies the search for genetic variation.
Using the new approach in the hydatidiform genome, the researchers were able to
identify and sequence 26,079 segments that were different from a standard human
reference genome used in genome research. Most of these variants, about 22,000,
have never been reported before, Eichler said.
"These findings suggest that there is a lot of variation we are missing," he said.

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The technique also allowed Eichler and his colleagues to map some of the more than
160 segments of the genome, called euchromatic gaps, that have defied previous
sequencing attempts. Their efforts closed 50 of the gaps and narrowed 40 others.

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The gaps include some important sequences, Eichler said, including parts of genes
and regulatory elements that help control gene expression. Some of the DNA
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Eichler said, "It is likely that if a sequence of this DNA were put into an E. coli, the
bacteria would delete the DNA." This may explain why it could not be sequenced
using standard approaches. He added that the gaps also carry complex sequences

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that are not well reproduced by standard sequencing technologies.

"The sequences vary extensively between people and are likely hotspots of genetic
instability," he explained.
For now, SMRT technology will remain a research tool because of its high cost, about
$100,000 per genome.
Eichler predicted, "In five years there might be a long-read sequence technology that
will allow clinical laboratories to sequence a patient's chromosomes from tip to tip and
say, 'Yes, you have about three to four million SNPs and insertions deletions but you
also have approximately 30,000-40,000 structural variants. Of these, a few structural
variants and a few SNPs are the reason why you're susceptible to this disease.'
Knowing all the variation is going to be a game changer."

The above story is based on materials provided by University of Washington Health

Sciences/UW Medicine. Note: Materials may be edited for content and length.
Journal Reference:
1. Mark J. P. Chaisson, John Huddleston, Megan Y. Dennis, Peter H. Sudmant,
Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard
Sandstrom, Matthew Boitano, Jane M. Landolin, John A. Stamatoyannopoulos,
Michael W. Hunkapiller, Jonas Korlach, Evan E. Eichler. Resolving the
complexity of the human genome using single-molecule sequencing.
Nature, 2014; DOI: 10.1038/nature13907

Chicago

University of Washington Health Sciences/UW Medicine. "Thousands of neverbefore-seen human genome variations uncovered." ScienceDaily. ScienceDaily, 10
November 2014. <www.sciencedaily.com/releases/2014/11/141110124233.htm>.

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