A4 T H E BULLETIN • TUESDAY, NOVEMBER 13, 2012
Genes
IN BRIEF Part of Long Island still dark after Sandy HICKSVILLE, N.Y. — Two weeks after Superstorm Sandy, while most utilities have restored electricity to nearly all their customers, there was
one glaring exception: a Long Island power company with more outages— almost 60,000 Monday — than all the others combined. As people on Long Island fumed over the cold and the darkness an d c o m plained that they couldn't get answers from the company, the Long Island Power Authority said in its defense that the storm was worse than anyone could have imagined and that it d i dn't just damage outdoor electrical lines; it caused flooding that touched home and business breaker boxes.
2 BBC executives step aside temporarily L ONDON — T h e BB C s truggled Monday t o c o n tain a spreading crisis over its reporting of a decades-old sexual abuse scandal as two senior executives withdrew temporarily from t heir j obs following the resignation of the corporation's director-general, a move that encapsulated the worst setback to the public broadcaster's status, prestige and selfconfidence foryears. The BBC's website said its director of news, Helen Boaden, and her deputy, Stephen Mitchell, had "stepped aside," the latest moves since a flagship current affairs program, "Newsnight," wrongly implicated a former Conservative Party politician in accusations of sexualabuse at a children's home in North Wales in the 1970s and 1980s. The BBC management said that neither Boaden nor Mitchell "had anything at all to do with the f ailed 'Newsnight' investigation" of the politician, Alistair McAlpine. But it "believes there is a lack of clarity in the lines of command and control in BBC News" because of an inquiry into a separate "Newsnight" debacle — the cancellation of a program a year ago into allegations of sexual abuse by Jimmy Savile, a longtime BBC television host who died last year at age 84.
Indiana blast inquiry focuses on natural gas I NDIANAPOLIS — Th e search for what caused a massive, deadly explosion that rocked an Indianapolis neighborhood turned to natural gas Monday, with officials checking gas lines and a h omeowner saying a problem furnace couldbe to blame. The National Transportation Safety Board sent investigators to check gas main and other lines serving the neighborhood where tw o p eople were killed and seven injured in the weekend blast. Local gas supplier Citizens Energy said it also was checking gas lines and a meter at the home that exploded. But officials cautioned that it was too soon to rule out other causes, saying only that they do not believe a meth lab was to blame for the explosion that obliterated two h omes and severely damaged dozens of others. — From wire reports
Continued from A1 It also holds out hope for eventual treatments, doctors
"Everyone who has a child with an unexplained condition should have access to this. We're at a point where anyone at a medical center with the right people can do this."
say. Babies with baffling conditions shouldhavelargeswaths of their D N A s e quenced, said scientists and doctors at the annual meeting of the American Society of Human Genetics in San Francisco last week. At least 50,000 babies born every year in the United States might benefit, said Jimmy Lin, a geneticist at Washington University in St. Louis. "Everyone who has a child with an unexplained condition should have access to this," said Lin, who established the Rare Genomics Institute to help families pay for their children's sequencing when insurers won't. "We're at a point where anyone at a medical center with the right people can do this."
'Matter of time' While the excitement of solving genetic riddles runs high, the power of sequencing babies also raises concerns. Only in rare cases does knowing the genetic cause of a condition lead to better, let alone any, treatment. Still, parents can at least know what is wrong, and the
hope is that by mapping a baby's genes, scientists may eventually find cures, doctors say. "It's just a matter of time until this becomes a first- line test for babies with undiagnosed disorders," said Columbia University geneticist Wendy Chung. "As costs fall and insurers become more comfortable, this will become the go-to test." The human genome is a code for makingall thebody's cells and proteins. Sequencing all the relevant portion of a child's DNA costs about $2,500, said Lin, at Washington University. That's a fraction of the bill for a day in the neonatal intensive care unit — about $8,000, he said. For Patrick Butters and his parents, who live in East Setauket, N.Y., the new approach meant finally solving th e f a m ily's m edical mystery. Unexplained tumors had tormented Patrick's mother, Melissa, since her birth in 1976. At the time, she had four small growths in her cheek, upper back, armpit and abdomen. Three were cut out, and the one in her cheek, which was never removed, disappeared on its own by the time she was four, leaving her with a small dimple. Melissa's doctors were stumped. Norma W ollnerSternberg, Melissa's pediatric oncologist at M emorial Sloan-Kettering Cancer Center in New York, said she wasn't sure at the time whether Melissa's condition was inherited or whether it would worsen. As Melissa grew, her tumors recurred less frequently and presentedfew problems. She remained healthy and active, and now practices law in her community. After discussions with her husband, it seemed reasonable to have a child. In 2010, to be on the safe side, Melissa approached Columbia's Chung about using DNA analysis to get to the bottom of the condition.
— Jimmy Lin, geneticist
Chung analyzed Melissa's DNA, looking for mutations in genes that were already known to cause the types of tumors that had appeared in her body over the years. The tests yielded nothing. When Patrick was born without any g r owths, the B utters f amily w e r e r e lieved. Then, the first tumor appeared in hi s abdomen. Samples from Patrick's and Melissa's tumors were sent them to H a rvard-affiliated Brigham and Women's Hospital in Boston, where they were classified for the first time as myofibromas, a type of connective-tissue tumor that usually strikes children. The Butters family is insuredby Cigna Corp. through Chris's employer, a software company, which paid for Patrick's treatment. Chung paid for Patrick's sequencing using about $1,000 in research funds along with time from her colleagues that wasn't reimbursed. After P a t r ick's i n i t i al t umor wa s r e moved, hi s parents found eight more growths on Patrick's head, left shoulder and back. Then, in July, Melissa was playing in the pool with Patrick when he yawned, revealing something unfamiliar and white in his mouth. She looked more closely and reached in with her finger, touching what appeared to be a new growth. Picking up Patrick, Butters rushed to the phone to call his pediatrician. She referred Butters to an ear, nose and throat surgeon, who advised taking Patrick to Memorial Sloan-Kettering as soon as
possible. Patrick was seen by a pediatric surgeon, and within a week, he was in the operating room having the growth removed.
Hunting a cause More and more, the parents were anxious to find out whether the tumors were inherited, and if so, which m utation wa s b e h ind i t . While it was unlikely they'd be able to seek treatment, they hoped the information could be used so that Melissa, or even Patrick, might have a child that wouldn't be affected by the mysterious condition. Chung, at Columbia, redoubled her efforts to find the source ofthe problem, tapping into technology that was making the hunt f or DNA mutations faster every month. She sent samples from Patrick's case to the Columbia Genome Center,opened 18 months ago and run by Olivier Couronne, a computer scientist who had worked on the Human Genome Project. The volume of work done by the center is increasing by a third to a half every three months, he said. Samples come to Columbia's sequencers from across the U.S. and five other countries. Couronne analyzed the Patrick's samples with a process that is rapidly becoming a leading approach to diag-
nosing unknown conditions, calledRNASeq. Thetechnique focuses on a complementary moleculeto DNA, called RNA, which tells cells exactly which proteins to make. By looking for flaws in RNA, scientists can sometimes quickly backtrack to corresponding DNA mutations. The analysis yielded almost 7,000 genes in Patrick's tumors that appeared to vary from known, healthy DNA sequences. While most of these would turn out to be normal variations in DNA and posed no danger, any one of these mutations might be the one that caused the tumors in Melissa and Patrick. To determine which w as causing t h e un e x p lained growths, Columbia scientists then used computer databases of known genes that might be related to tumors like those seen in the Butterses. The researchers quickly narrowed the list to about 10. Then they found the culprit. The most likely genes to be associated with their myofibroma tumors was called PDGFRB, named for its product, a protein called plateletderived growth factorreceptor. It's been related to tumors before. All Patrick's tumors have at least one mutation in the gene. Melissa has a mutation in the same PDGFRB gene. Neither of her parents did. That meant the m u tation l i k ely took place at some point during M e l i ssa's c o nception, Chung said. Patrick inherited that mutation. Late one evening in September, Chung e-mailed Melissa to say that she had located the flaw in the PDGFRB gene. She then reached out to about a half-dozen doctors worldwide who had reported similar disorders in their patients. Did those patients have mutations that matched the Butterses"? The answer came t h r ee weeks ago. A family in Australia and another family that had been analyzed by McGill University scientists in Montreal had the same tumor disorder and the same mutation. The Butters' medical mystery was solved. Now that the gene had been located, what could they do'? While doctors said t h ey c ouldn't stop P atrick's t u mors fro m g r o w ing, t h ey could prevent the mutation from being passed on to future children. SelfReferrals Welcome
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Water Continued from A1 T he City C ouncil h a s not v oted o n wh e t h er to adopt th e c o mmittee recommendations. Currently, residents who pay for year-round water service are subsidizing the cost to keep water available at all times to vacant homes in foreclosureand part-time residents with second homes in B e nd. "The water users who are here, we don't really feel should be subsidizing the folks wh o a r e n't," s aid Frank Turek, an advisory committee member, during a Nov. 7 presentation to the City Council. Turek and other committee members said their rate proposal emphasizes fairness and equity among water users. They h ave been studying the f i x ed and variable costs of the water system to determine which costs increase when people use more water and which costs remain steady, regardless of how m uch water is used. For example, the cost to build a new water treatm ent plant w ould b e a fixed cost and should be divided among all water users asa flat fee,according to the committee. The cost of operating the plant would be variable, since it could rise or fall depending upon demand, so it should be f a ctored into the cost of each cubic foot of water, the committee found. C ommittee mem b e r Nancy Loveland said the city has an obligation to maintain at all times a supply of safe drinking water that is adequate to serve the community. The city must also meet state and federal water quality standards, and maintain "fireflows" necessary for crews to fight fires. "These costs are fixed," Loveland said. "We're saying all customers should get a fixed rate." C ommittee mem b e r Andy High, who i s al so vice president for government affairs at the Central Oregon Builders Association, said fires can occur in homes even when the owners are out of town for an extended time. Under the current system, those people do not pay for water to be available at all
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proposal from the Infrastructure Advisory Committee would shift
more revenueburden onto fixed charges, which it says
would more fairly distribute the burden of maintaining the water system and
charge users only for what they use. How this would affect individual ratepayers' bills is not yet clear.
REVENUEALLOCATION Current P r oposed 56% Fixed costs62%
44% Rated costs38% Source: City of Bend Andyzeigert/The Bulletin
times to fight the fire. City Councilor Mark C apell said it i s c ounterintuitive that people who use little water could actually see their bills increase under a system based more on water usage. T urek a greed, bu t s a i d some of thelarger water users mighthave been subsidizing the fixed costs in the water system. F inance D i r ector S o n i a A ndrews said e a rlier t h i s year that a new water rate structure could take effect in January if the City Council approves. That would be the second rate change to hit residents in one year; rates increased on July I to pay for improvements to the w ater and sewer systems. — Reporter: 541-617-7829, hborrud@bendbulletin.com
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