
At the most basic level cancer can be defined as the DNA of a normal cell going haywire.
One way that DNA can go haywire is through something called aneuploidy, where one or more of a cell’s 23 chromosomes gets duplicated. It can also commonly happen through structural variations in the sequences within the DNA — think of the double helix model from middle school science then move around the pieces.
Those changes can occur in any of the 3.2 billion base pairs of DNA found in each person. That means the data sets holding genome sequences for cancer cells can be huge.
Usually those changes are looked at separately, but Carnegie Mellon University Associate Professor of Computational Biology Jian Ma is using servers at CMU to crunch data to see how aneuploidy mutations and structural variations relate to each other.
“The advantage, of course, is if you look at them together, you can identify these event more precisely in an unbiased way,” Ma said. “You will be able to tell the timing of these event so you will be able to know if this structure rearrangement happened before chromosome duplication or after chromosome duplication.”
Ma is doing this by looking at breast and cervical cancer genomes that have already been sequenced as part of the Cancer Genome Atlas. The Atlas is a federally-funded project to catalog the genetic mutations responsible for cancer.
“As a computational biologist, our interest is to develop new algorithms, new analytic tools, that can look at these data from different perspective and then you can potentially identify new things that are relevant to the biology of cancer,” said Ma, who is pushing that huge data set through code that he calls “Weaver.”
Adrian Lee, a professor of pharmacology and chemical biology at the University of Pittsburgh, said medicine keeps producing bigger and bigger data sets.
“And so now we are virtually dependent on computational biology to try to decipher what these changes mean,” Lee said. “Say you find a million changes, but only 20 are important. How do you find those 20? It’s kind of a needle in a haystack.”
Cancer evolves over time. Two biopsies taken of the same cancer, from the same patient, a year apart would look different on the DNA level, Lee said.
“We can measure the DNA and then try to build models to predict how it changed over time and then what it would have done in the future,” Lee said. “In that way we can predict how it’s going to change and then what we should target.”
Ma’s code was published in the journal Cell Systems and he said hopes scientists will use it on other data sets. Weaver has already found some duplicated chromosomal regions that are caused by specific structural variations.
Ma said he hopes to improve his algorithms to better understand those evolutions and then apply it to more samples from the Cancer Genome Atlas project. From there it could move into the clinical setting.
“Weaver at the moment is just an algorithm, there is no direct clinical impact yet,” Ma said. “But I think I will be interested in exploring potential opportunities like how to apply Weaver in the broader context.”
Researchers said someday this type of big data crunching could help doctors tailor a specific treatment to a patient’s specific cancer mutation.
This article was originally published on wesa.fm can be viewed in full


Archive
- October 2024(44)
- September 2024(94)
- August 2024(100)
- July 2024(99)
- June 2024(126)
- May 2024(155)
- April 2024(123)
- March 2024(112)
- February 2024(109)
- January 2024(95)
- December 2023(56)
- November 2023(86)
- October 2023(97)
- September 2023(89)
- August 2023(101)
- July 2023(104)
- June 2023(113)
- May 2023(103)
- April 2023(93)
- March 2023(129)
- February 2023(77)
- January 2023(91)
- December 2022(90)
- November 2022(125)
- October 2022(117)
- September 2022(137)
- August 2022(119)
- July 2022(99)
- June 2022(128)
- May 2022(112)
- April 2022(108)
- March 2022(121)
- February 2022(93)
- January 2022(110)
- December 2021(92)
- November 2021(107)
- October 2021(101)
- September 2021(81)
- August 2021(74)
- July 2021(78)
- June 2021(92)
- May 2021(67)
- April 2021(79)
- March 2021(79)
- February 2021(58)
- January 2021(55)
- December 2020(56)
- November 2020(59)
- October 2020(78)
- September 2020(72)
- August 2020(64)
- July 2020(71)
- June 2020(74)
- May 2020(50)
- April 2020(71)
- March 2020(71)
- February 2020(58)
- January 2020(62)
- December 2019(57)
- November 2019(64)
- October 2019(25)
- September 2019(24)
- August 2019(14)
- July 2019(23)
- June 2019(54)
- May 2019(82)
- April 2019(76)
- March 2019(71)
- February 2019(67)
- January 2019(75)
- December 2018(44)
- November 2018(47)
- October 2018(74)
- September 2018(54)
- August 2018(61)
- July 2018(72)
- June 2018(62)
- May 2018(62)
- April 2018(73)
- March 2018(76)
- February 2018(8)
- January 2018(7)
- December 2017(6)
- November 2017(8)
- October 2017(3)
- September 2017(4)
- August 2017(4)
- July 2017(2)
- June 2017(5)
- May 2017(6)
- April 2017(11)
- March 2017(8)
- February 2017(16)
- January 2017(10)
- December 2016(12)
- November 2016(20)
- October 2016(7)
- September 2016(102)
- August 2016(168)
- July 2016(141)
- June 2016(149)
- May 2016(117)
- April 2016(59)
- March 2016(85)
- February 2016(153)
- December 2015(150)