Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression.
Published in Bioinformatics
Evaluation of the SNP tagging approach in an independent population sample—array-based SNP discovery in Sami.
Published in Human Genetics
Significant efforts have been made to determine the correlation structure of common SNPs in the human genome. One method has been to identify the sets of tagSNPs that capture most of the genetic variation. Here, we evaluate the transferability of tagSNPs between populations using a population sample of Sami, the indigenous people of Scandinavia. Ar...
Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21.
...Published in Science
Global patterns of human DNA sequence variation (haplotypes) defined by common single nucleotide polymorphisms (SNPs) have important implications for identifying disease associations and human traits. We have used high-density oligonucleotide arrays, in combination with somatic cell genetics, to identify a large fraction of all common human chromos...
Decoding the human genome.
Published in Genome Research
Analysis of chromosome 22 deletions in neurofibromatosis type 2-related tumors.
Published in The American Journal of Human Genetics
The neurofibromatosis type 2 (NF2) gene has been hypothesized to be a recessive tumor suppressor, with mutations at the same locus on chromosome 22 that lead to NF2 also leading to sporadic tumors of the types seen in NF2. Flanking markers for this gene have previously been defined as D22S1 centromeric and D22S28 telomeric. Identification of subreg...
Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationshi...
...Published in Blood Cancer Journal
We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarte...
VISTA: computational tools for comparative genomics.
Published in Nucleic Acids Research
Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genom...
Active conservation of noncoding sequences revealed by three-way species comparisons.
Published in Genome Research
Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human-mouse DNA comparison studies have discovered numerous conserved noncoding sequences of which only a fraction has been functionally investigated A question therefore remains as to whether most of...
A novel and rapid method for isolating sequences adjacent to rare cutting sites and their use in physical mapping.
Published in Nucleic Acids Research
We describe a simple PCR based technique which can be used to isolate sequences adjacent to rare cutter sites and can subsequently be employed for the construction of long range physical maps. The method involves the ligation of an adaptor to rare cutter sequences and its use as a target for forward priming in PCR. Primers to Alu repeat elements in...
Elucidating the role of 8q24 in colorectal cancer.
Published in Nature Genetics
