The genetic landscape of the childhood cancer medulloblastoma
Authors:
D Williams Parsons, Meng Li, Xiaosong Zhang, Siân Jones, Rebecca J Leary, Jimmy Cheng-Ho Lin, Simina M Boca, Hannah Carter, Josue Samayoa, Chetan Bettegowda, Gary L Gallia, George I Jallo, Zev A Binder, Yuri Nikolsky, James Hartigan, Doug R Smith, Daniela S Gerhard, Daniel W Fults, Scott VandenBerg, Mitchel S Berger, Suely Kazue Nagahashi Marie, Sueli Mieko Oba Shinjo, Carlos Clara, Peter C Phillips, Jane E Minturn, Jaclyn A Biegel, Alexander R Judkins, Adam C Resnick, Phillip B Storm, Tom Curran, Yiping He, B Ahmed Rasheed, Henry S Friedman, Stephen T Keir, Roger McLendon, Paul A Northcott, Michael D Taylor, Peter C Burger, Gregory J Riggins, Rachel Karchin, Giovanni Parmigiani, Darell D Bigner, Hai Yan, Nick Papadopoulos, Bert Vogelstein, Kenneth W Kinzler, Victor E Velculescu
Journal:
Science. 2011 Jan 28;331(6016):435-9. doi: 10.1126/science.1198056. Epub 2010 Dec 16.
Abstract:
Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and sequenced all known protein-coding genes and microRNA genes using Sanger sequencing in a set of 22 MBs. We found that, on average, each tumor had 11 gene alterations, fewer by a factor of 5 to 10 than in the adult solid tumors that have been sequenced to date. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone-lysine N-methyltransferase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.
Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules
Authors:
Yuxuan Wang, Christopher Douville, Joshua D Cohen, Austin Mattox , Sam Curtis, Natalie Silliman, Maria Popoli, Janine Ptak, Lisa Dobbyn, Nadine Nehme, Jonathan C Dudley, Mahmoud Summers, Ming Zhang, Lan T Ho-Pham, Bich N H Tran, Thach S Tran, Tuan V Nguyen, Chetan Bettegowda, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein
Journal:
The Proceedings of the National Academy of Sciences, August 2023
Abstract:
The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.