Genomes and Genes
Pui Yan Kwok
Affiliation: Washington University School of Medicine
- Approaches to allele frequency determinationP Y Kwok
Washington University School of Medicine, St Louis, MO 63110, USA
Pharmacogenomics 1:231-5. 2000..Accurate and efficient allele frequency estimation in DNA pools will reduce the cost and effort needed in genetic and association studies and opens up ways to perform pharmacogenomic and evolutionary studies efficiently...
- High-throughput genotyping assay approachesP Y Kwok
Washington University School of Medicine, St Louis, MO 63110, USA
Pharmacogenomics 1:95-100. 2000..With the biochemistry for robust genotyping in place, good engineering solutions are needed to make high-throughput genotyping a reality...
- Methods for genotyping single nucleotide polymorphismsP Y Kwok
Washington University School of Medicine, St Louis, Missouri 63110, USA
Annu Rev Genomics Hum Genet 2:235-58. 2001..Judging from the accelerated pace of new method development, it is hopeful that an ideal SNP genotyping method will be developed soon...
- SNP genotyping with fluorescence polarization detectionPui Yan Kwok
Division of Dermatology and Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
Hum Mutat 19:315-23. 2002..Moreover, inexpensive, unpurified, and unlabeled probes are used in the primer extension reaction with FP detection. As an end-point detection mechanism, FP detection is suitable for high-throughput SNP genotyping...
- Pharmacogenomic assessment of carboxylesterases 1 and 2Sharon Marsh
Department of Medicine, Washington University School of Medicine and the Siteman Cancer Center, St Louis, MO 63110, USA
Genomics 84:661-8. 2004..Functional analysis of the novel polymorphisms described in this study is now warranted to identify putative roles in drug metabolism...
- Novel immunoglobulin superfamily gene cluster, mapping to a region of human chromosome 17q25, linked to psoriasis susceptibilityRebecca A Speckman
Departments of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
Hum Genet 112:34-41. 2003..The second was a three-locus haplotype lying within the first intron of CMRF35A2 ( TREM5) (TDT P=0.04). The novel markers described here will facilitate additional linkage and association studies between the CMRF35 family and disease...
- A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasisCynthia Helms
Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
Nat Genet 35:349-56. 2003..This is the second example of loss of a RUNX1 binding site associated with susceptibility to an autoimmune disease. It also suggests defective regulation of SLC9A3R1 or NAT9 by RUNX1 as a susceptibility factor for psoriasis...
- Localization of PSORS1 to a haplotype block harboring HLA-C and distinct from corneodesmosin and HCRCynthia Helms
Department of Genetics, Washington University School of Medicine, Box 8232, 4566 Scott Avenue, St Louis, Missouri, 63110, USA
Hum Genet 118:466-76. 2005..The introduction of a potential binding site for the RUNX/AML family of transcription factors in intron 7, is also specific to these HLA-C alleles. These variants need to be investigated further for their role as PSORS1...
- Identification of NR1I2 genetic variation using resequencingCristi R King
Department of Medicine, Washington University School of Medicine, St Louis, MO, 63110, USA
Eur J Clin Pharmacol 63:547-54. 2007..This heterodimer binds to the nuclear receptor response elements of downstream genes such as ABCB1, CYP2C, and CYP3A. This study determined the extent of NR1I2 variation in three world populations...
- A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease lociYing Liu
Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
PLoS Genet 4:e1000041. 2008..This region harbors the interleukin 2 (IL2) and interleukin 21 (IL21) genes and was recently shown to be associated with four autoimmune diseases (Celiac disease, Type 1 diabetes, Grave's disease and Rheumatoid Arthritis)...
- Role of excess inorganic pyrophosphate in primer-extension genotyping assaysMing Xiao
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143-0130, USA
Genome Res 14:1749-55. 2004..With this new protocol, we have achieved approximately 95% success rate in assay development without the need for optimization...
- Single-molecule analysis for molecular haplotypingPui Yan Kwok
Department of Dermatology, University of California, San Francisco 94143 0130, USA
Hum Mutat 23:442-6. 2004..In this work, we present the outline of the major challenges one must meet in developing a robust strategy for SNP detection and molecular haplotyping using single molecule analysis...
- Primer design for PCR and sequencing in high-throughput analysis of SNPsEllen F Vieux
Division of Dermatology, Washington University School of Medicine, St Louis, MO 63110, USA
Biotechniques . 2002..However, over 23,000 assays, including 96% of those recently analyzed, have been experimentally successfuL Similar design methods could be usedfor PCR assays in any organism with substantial available sequence...
- High-throughput genotyping with primer extension fluorescent polarization detectionPui-Yan Kwok
University of California, San Francisco, California, USA
Curr Protoc Hum Genet . 2004..When a fluorescently labeled nucleotide is incorporated, high FP is observed for that dye and the genotype of the DNA sample is determined...
- Natural variation in four human collagen genes across an ethnically diverse populationTing Fung Chan
Cardiovascular Research Institute and Institute for Human Genetics, University of California at San Francisco, San Francisco, CA 94143, USA
Genomics 91:307-14. 2008..Our observations suggest that the study of collagen mutations and their relationships with disease phenotypes should be performed in the context of the genetic background of the subjects...
- Common beta-adrenergic receptor polymorphisms are not associated with risk of sudden cardiac death in patients with coronary artery diseaseZian H Tseng
Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, University of California, San Francisco, USA
Heart Rhythm 5:814-21. 2008....
- Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levelsDavid Reich
Department of Genetics, Harvard Medical School, New Research Building, Boston, MA 02115, USA
Am J Hum Genet 80:716-26. 2007..0x10-12 for IL-6 SR, and P<2.0x10-9 for IL-6. These results also serve as an important proof of principle, showing that admixture mapping can not only coarsely localize but can also fine map a phenotypically important variant...
- Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysisGoncalo Abecasis
Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
Nat Genet 39:153-5. 2007..The meeting highlighted recent advances in characterization of genetic variation, including genome-wide association studies and structural variation...
- A simple DNA stretching method for fluorescence imaging of single DNA moleculesTing-Fung Chan
Cardiovascular Research Institute, University of California, San Francisco CA, USA
Nucleic Acids Res 34:e113. 2006..The very low background fluorescence allows efficient detection of single fluorescent dye labels incorporated into the stretched DNA molecules...
- Genome-wide association studies getting more complicated but help is on the wayPui-Yan Kwok
Hum Genomics 2:341-2. 2006
- Adrenoceptor polymorphisms and the risk of cardiac injury and dysfunction after subarachnoid hemorrhageJonathan G Zaroff
Department of Medicine, University of California, San Francisco, USA
Stroke 37:1680-5. 2006..We hypothesized that adrenoceptor polymorphisms resulting in greater catecholamine sensitivity would be associated with an increased risk of cardiac injury...
- Apolipoprotein E epsilon 2 is associated with new hemorrhage risk in brain arteriovenous malformationsLudmila Pawlikowska
The Cardiovascular Research Institute, University of California, San Francisco 94110, USA
Neurosurgery 58:838-43; discussion 838-43. 2006..Identification of genetic variants associated with increased new ICH risk would facilitate risk stratification and guide therapeutic intervention...
- Arteriovenous malformationWilliam L Young
J Neurosurg 106:731-2; author reply 732-3. 2007
- Determination of haplotypes from single DNA molecules: a method for single-molecule barcodingMing Xiao
Cardiovascular Research Institute and Center for Human Genetics, University of California, San Francisco, San Francisco, California
Hum Mutat 28:913-21. 2007..The feasibility of this technology is demonstrated by the determination of the haplotype of a 9.3-kbp DNA fragment containing four SNPs...
- Gene-trapped mouse embryonic stem cell-derived cardiac myocytes and human genetics implicate AKAP10 in heart rhythm regulationWhittemore G Tingley
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 104:8461-6. 2007..Our stem cell-based screen may provide a means of identifying other genes that control heart rhythm...
- An apolipoprotein A-V gene SNP is associated with marked hypertriglyceridemia among Asian-American patientsClive R Pullinger
Cardiovascular Research Institute, University of California, San Francisco, CA, USA
J Lipid Res 49:1846-54. 2008..This specific apoA-V variant has a pronounced effect on TG metabolism, the mechanism of which remains to be elucidated...
- A second generation human haplotype map of over 3.1 million SNPsKelly A Frazer
The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
Nature 449:851-61. 2007..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
- SNPs meet CNVs in genome-wide association studies: HGV2007 meeting reportXavier Estivill
Genes and Disease Program, Center for Genomic Regulation (CRG-UPF, Barcelona, Spain
PLoS Genet 4:e1000068. 2008
- Endothelial nitric oxide synthase polymorphism (-786T->C) and increased risk of angiographic vasospasm after aneurysmal subarachnoid hemorrhageNerissa U Ko
Department of Neurology, University of California, San Francisco, USA
Stroke 39:1103-8. 2008..Decreased availability of nitric oxide (NO) may be crucial in its pathogenesis. We hypothesized that endothelial NO synthase (eNOS) polymorphisms may determine susceptibility to vasospasm in SAH patients...
- Genome-wide detection and characterization of positive selection in human populationsPardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007....
- Association of tumor necrosis factor-alpha-238G>A and apolipoprotein E2 polymorphisms with intracranial hemorrhage after brain arteriovenous malformation treatmentAchal S Achrol
Center for Cerebrovascular Research and Department of Anesthesia and Perioperative Care, University of California, San Francisco, California 94110, USA
Neurosurgery 61:731-9; discussion 740. 2007..We hypothesized that the risk of posttreatment ICH would also be greater in patients with brain arteriovenous malformations with these genotypes...
- Seventh international meeting on single nucleotide polymorphism and complex genome analysis: 'ever bigger scans and an increasingly variable genome'Dominique Rocha
Genus Cambridge Research Laboratory, University of Cambridge, Department of Pathology, Genus plc, Tennis Court Road, CB2 1QP, Cambridge, UK
Hum Genet 119:451-6. 2006..Overall, there have been a number of recent advances in genomics that promise to accelerate the pace of dissecting the genetic basis of many complex diseases in humans-and perhaps in other species...
- Distribution of human SNPs and its effect on high-throughput genotypingDaniel C Koboldt
Department of Genetics, Washington University, St. Louis, Missouri, USA
Hum Mutat 27:249-54. 2006..We found that assays with such primer site mutations were correlated with elevated rates of genotype failure and allele dropout. This suggests that taking nearby SNPs into account is important for optimal genotyping assay design...
- Tumor necrosis factor-alpha-238G>A promoter polymorphism is associated with increased risk of new hemorrhage in the natural course of patients with brain arteriovenous malformationsAchal S Achrol
Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA
Stroke 37:231-4. 2006....
- ADAM33 is not associated with asthma in Puerto Rican or Mexican populationsDenise L Lind
University of California at San Francisco, San Francisco, CA 94143-0833, USA
Am J Respir Crit Care Med 168:1312-6. 2003..We conclude that the ADAM33 gene is not an important risk factor for asthma or for asthma-associated phenotypes in Mexicans or in Puerto Ricans...
- Detection of single nucleotide polymorphismsPui Yan Kwok
Cardiovascular Research Institute, University of California, 505 Parnassus Avenue, Long 1332A, Box 0130, San Francisco, CA 94143 0130, USA
Curr Issues Mol Biol 5:43-60. 2003..Despite the considerable gains over the last decade, new approaches must be developed to lower the cost and increase the speed of SNP detection...
- DNA analysis by fluorescence quenching detectionMing Xiao
Cardiovascular Research Institute and the Department of Dermatology, University of California, San Francisco, California 94143, USA
Genome Res 13:932-9. 2003..993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations...
- Efficient high-throughput resequencing of genomic DNARaymond D Miller
Washington University, Division of Dermatology, St. Louis, Missouri 63110, USA
Genome Res 13:717-20. 2003..SNP primers and characterization results are provided at http://snp.wustl.edu...
- Kinetic FP-TDI assay for SNP allele frequency determinationMing Xiao
Washington University School of Medicine, St. Louis, MO, USA
Biotechniques 34:190-7. 2003..The accuracy of allele frequency determination with pooled samples is within 3.3 +/- 0.8% of that determined by genotyping individual samples that make up the pool...
- Homogeneous primer extension assay with fluorescence polarization detectionTony M Hsu
Division of Dermatology, Washington University, St. Louis, MO, USA
Methods Mol Biol 212:177-87. 2003
- SNP discovery by direct DNA sequencingPui-Yan Kwok
Cardiovascular Research Institute, Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
Methods Mol Biol 212:71-84. 2003
- Making 'random amplification' predictable in whole genome analysisPui Yan Kwok
University of California, San Francisco, 505 Parnassus Ave, Long 1332A, Box 0130, San Francisco, CA 94118, USA
Trends Biotechnol 20:411-2. 2002....
- Polymorphisms in genes involved in inflammatory and angiogenic pathways and the risk of hemorrhagic presentation of brain arteriovenous malformationsLudmila Pawlikowska
Cardiovascular Research Institute, University of California, San Francisco, Calif 94110, USA
Stroke 35:2294-300. 2004..Identification of genetic polymorphisms associated with ICH would facilitate risk stratification in BAVM patients...
- Variations in human HM74 (GPR109B) and HM74A (GPR109A) niacin receptorsChristian Zellner
Cardiovascular Research Institute, University of California, San Francisco 94143 0130, USA
Hum Mutat 25:18-21. 2005..Haplotype analysis suggests four SNPs can define the five major haplotypes that lie within a single haplotype block encompassing these two genes...
- Genetic admixture and asthma-related phenotypes in Mexican American and Puerto Rican asthmaticsKeyan Salari
Department of Medicine, University of California, San Francisco, California 94143-1732, USA
Genet Epidemiol 29:76-86. 2005..These results suggest that asthma severity may be influenced by genetic factors differentiating Europeans and Native Americans in Mexican Americans, although differing results for Puerto Ricans require further investigation...
- Population stratification confounds genetic association studies among LatinosShweta Choudhry
University of California, San Francisco, 94143-0833, USA
Hum Genet 118:652-64. 2006..Our findings suggest that empirical assessment of the effects of stratification is critical to appropriately interpret the results of case-control studies in admixed populations...
- Interleukin-6 involvement in brain arteriovenous malformationsYongmei Chen
Center for Cerebrovascular Research, University of California at San Francisco, 1001 Potrero Avenue, San Francisco, CA, USA
Ann Neurol 59:72-80. 2006....
- Polymorphism discovery in 51 chemotherapy pathway genesRobert R Freimuth
Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
Hum Mol Genet 14:3595-603. 2005..These results provide experimental validation and estimated allele frequencies for polymorphisms in three common ethnic groups and facilitate applied pharmacogenetic studies of anticancer drugs...
- Population structure, admixture, and aging-related phenotypes in African American adults: the Cardiovascular Health StudyAlexander P Reiner
Department of Epidemiology, University of Washington, Seattle, WA 98101 1448, USA
Am J Hum Genet 76:463-77. 2005..Complementary methods that identify discrete subgroups on the basis of genetic similarity may help to further characterize the complex biodemographic structure of human populations...
- Polymorphisms in transforming growth factor-beta-related genes ALK1 and ENG are associated with sporadic brain arteriovenous malformationsLudmila Pawlikowska
Cardiovascular Research Institute, University of California, San Francisco, CA 94110, USA
Stroke 36:2278-80. 2005..We investigated whether polymorphisms in these genes are also associated with sporadic BAVM...
- Lack of support for the association between GAD2 polymorphisms and severe human obesityMichael M Swarbrick
Diabetes Center, University of California, San Francisco, California, USA
PLoS Biol 3:e315. 2005....
- Kinetic fluorescence-quenching detection assay for allele frequency estimationMing Xiao
Cardiovascular Research Institute, University of California, San Francisco, CA, USA
Methods Mol Biol 311:115-23. 2005..993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations...
- High-density single-nucleotide polymorphism maps of the human genomeRaymond D Miller
Washington University, Division of Dermatology, St. Louis, MO, USA
Genomics 86:117-26. 2005..A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available...
- Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide polymorphism haplotypingJian-Bing Fan
Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
Genomics 79:58-62. 2002....