RT Journal
A1 Dai, Zunyan
A1 Weichenhan, Dieter
A1 Wu, Yue-Zhong
A1 Hall, Julia L
A1 Rush, Laura J.
A1 Smith, Laura T.
A1 Raval, Aparna
A1 Yu, Li
A1 Kroll, Daniela
A1 Muehlisch, Joerg
A1 Frühwald, Michael C.
A1 de Jong, Pieter
A1 Catanese, Joe
A1 Davuluri, Ramana V.
A1 Smiraglia, Dominic J.
A1 Plass, Christoph
T1 An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands
JF Genome Research 
JO Genome Research 
YR 2002 
FD October 01 
VO 12 
IS 10 
SP 1591 
OP 1598 
DO 10.1101/gr.197402 
UL http://genome.cshlp.org/content/12/10/1591.abstract 
AB Knudson's two-hit hypothesis postulates that genetic alterations in both alleles are required for the inactivation of tumor-suppressor genes. Genetic alterations include small or large deletions and mutations. Over the past years, it has become clear that epigenetic alterations such as DNA methylation are additional mechanisms for gene silencing. Restriction Landmark Genomic Scanning (RLGS) is a two-dimensional gel electrophoresis that assesses the methylation status of thousands of CpG islands. RLGS has been applied successfully to scan cancer genomes for aberrant DNA methylation patterns. So far, the majority of this work was done using NotI as the restriction landmark site. Here, we describe the development of RLGS using AscI as the restriction landmark site for genome-wide scans of cancer genomes. The availability of AscI as a restriction landmark for RLGS allows for scanning almost twice as many CpG islands in the human genome compared with using NotI only. We describe the development of an AscI–EcoRV boundary library that supports the cloning of novel methylated genes. Feasibility of this system is shown in three tumor types, medulloblastomas, lung cancers, and head and neck cancers. We report the cloning of 178 AscI RLGS fragments via two methods by use of this library.[Supplemental material is available online at http://www.genome.org.]