Bringing genomics to cancer
detection and surveillance
By Eva Emerson
A new way to identify cancer’s genetic
scrambling may allow doctors to better
monitor how patients respond to treatment and detect a tumor recurrence.
Wholesale juggling of chunks of DNA
is common in cancer cells, but cataloging those changes hasn’t been easy. Now,
a small study of colorectal and breast
tumor cells shows that these genetic
rearrangements can be reliably identified and that these genetic changes
are unique to each individual’s tumor.
While that individuality may stymie
efforts to design therapies to target these
rearrangements, their presence alone
can be useful as a marker of cancer’s
waxing and waning, scientists reported
at a news briefing February 18 and in the
Feb. 24 Science Translational Medicine.
The ability to rapidly identify such
rearrangements from individual tumors
offers doctors a potentially powerful way
to track tumor activity in patients.
In a commentary in the same issue,
Ludmila Prokunina-Olsson and Stephen
Chanock of the National Cancer Institute in Bethesda, Md., say the new study
“lays an important foundation,” but
caution that some issues still need to be
worked out before the next-generation
method used in the study becomes a
“this-generation” medical tool.
Though the cost per patient — the team
spent about $5,000 characterizing the
specific genetic changes in each of the
six people studied — is still high, most
believe it will drop fairly quickly, said
study author Victor Velculescu of the
Kimmel Cancer Center at Johns Hopkins
University in Baltimore. He is optimistic the work will lead to a commercially
available blood test in a few years.
Tracking chunky rearrangements in
tumor DNA (colon cancer cells above)
provides hints about patient health.
In the study, scientists from Johns
Hopkins and Life Technologies Corp. of
Foster City, Calif., compared the genomic
sequence from a tumor biopsy with that
of normal tissue taken from the same
person. Looking at four patients with
colorectal cancer and two with breast
cancer, scientists identified four to 17
unique genetic rearrangements in each
tumor. The rearrangements were dramatic in nature, Velculescu said, more
like “switching the order of chapters in a
book than a typo in a word in the text.”
The team found the rearrangements only
by using massively parallel sequencing
methods capable of reading hundreds
of millions of DNA letters and advanced
computers to analyze results.
Using custom-made DNA probes for
two patients, the team was able to detect
as little as one tumor DNA fragment in
400,000 normal DNA fragments. Scientists then tracked blood levels of the
tumor marker in one patient before and
after tumor surgery. Levels dropped after
surgery, only to rise again. After more
treatment, marker levels dropped substantially, but a small amount was still
detectable, consistent with a small part
of the tumor having spread. s
Marine reserve placement is key
Targeting heaviest-fished areas can boost conservation
By Alexandra Witze
Saving both fish and the fishermen who
depend on them appears to come down to
one thing: location, location, location.
Marine protected areas need to be
located in the right spots to have the
maximum effect, researchers report.
The work was presented on February 21
and appears in papers published online
February 22 in the Proceedings of the
National Academy of Sciences.
In the Black Sea, for instance, setting
aside just 20 to 30 percent of the most
affected areas within marine reserves
could accomplish nearly all the goals of
protecting the entire reserve, reported
a team led by Benjamin Halpern of the
National Center for Ecological Analysis
and Synthesis in Santa Barbara, Calif.
Precisely placing reserves, he said, “can
have a dramatic effect on their ability to
improve overall ocean health.”
Halpern’s work could also help
illuminate which areas are worth pro-
tecting. The biggest potential gain, he
said, comes in areas that are heavily
fished, where setting aside large chunks
led to ocean health improvements of up
to 50 percent.