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1 News 92 Publications 17 Members

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.

Clark, Rm Schweikert, G Toomajian, C Ossowski, S Zeller, G Shinn, P Warthmann, N Hu, Tt Fu, G Hinds, Da ...

Published in Science

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymor...

Whole-genome patterns of common DNA variation in three human populations.

Hinds, Da Stuve, Ll Nilsen, Gb Halperin, E Eskin, E Ballinger, Dg Kelly A. Frazer Cox, Dr

Published in Science

Individual differences in DNA sequence are the genetic basis of human variability. We have characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry. Our results indicate that these SNPs capture most common genetic variati...

Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional.

Kelly A. Frazer Tao, H Osoegawa, K De Jong, Pj Chen, X Doherty, Mf Cox, Dr

Published in Genome Research

Cross-species DNA sequence comparison is a fundamental method for identifying biologically important elements, because functional sequences are evolutionarily conserved, wheres nonfunctional sequences drift. A recent genome-wide comparison of human and mouse DNA discovered over 200,000 conserved noncoding sequences with unknown function. Multispeci...

The nature, pattern and function of human sequence variation.

Eichler, Ee Kelly A. Frazer

Published in Genome Biology

Fine-scale recombination patterns differ between chimpanzees and humans.

Ptak, Se Hinds, Da Koehler, K Nickel, B Patil, N Ballinger, Dg Przeworski, M Kelly A. Frazer Pääbo, S

Published in Nature Genetics

Recombination rates seem to vary extensively along the human genome. Pedigree analysis suggests that rates vary by an order of magnitude when measured at the megabase scale, and at a finer scale, sperm typing studies point to the existence of recombination hotspots. These are short regions (1-2 kb) in which recombination rates are 10-1,000 times hi...

Evaluation of the SNP tagging approach in an independent population sample—array-based SNP discovery in Sami.

Johansson, A Vavruch-Nilsson, V Cox, Dr Kelly A. Frazer Gyllensten, U

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.

Barrett, Wa Doshi, Jm Hacker, Cr Kautzer, Cr Lee, Dh Marjoribanks, C Mcdonough, Dp Nguyen, Bt Norris, Mc Sheehan, Jb ...

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.

Kelly A. Frazer

Published in Genome Research

Analysis of chromosome 22 deletions in neurofibromatosis type 2-related tumors.

Wolff, Rk Kelly A. Frazer Jackler, Rk Lanser, Mj Pitts, Lh Cox, Dr

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... PDF available through Get Fulltext Research

Erin N. Smith Ghia, Em Deboever, Cm Rassenti, Lz Jepsen, K Yoon, Ka Hiroko Matsui Rozenzhak, S Alakus, H Shepard, Pj ...

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...

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