Pui Yan Kwok

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. ncbi request reprint Approaches to allele frequency determination
    P Y Kwok
    Washington University School of Medicine, St Louis, MO 63110, USA
    Pharmacogenomics 1:231-5. 2000
  2. ncbi request reprint High-throughput genotyping assay approaches
    P Y Kwok
    Washington University School of Medicine, St Louis, MO 63110, USA
    Pharmacogenomics 1:95-100. 2000
  3. ncbi request reprint Methods for genotyping single nucleotide polymorphisms
    P Y Kwok
    Washington University School of Medicine, St Louis, Missouri 63110, USA
    Annu Rev Genomics Hum Genet 2:235-58. 2001
  4. ncbi request reprint SNP genotyping with fluorescence polarization detection
    Pui Yan Kwok
    Division of Dermatology and Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA
    Hum Mutat 19:315-23. 2002
  5. ncbi request reprint Polymorphism discovery in 51 chemotherapy pathway genes
    Robert R Freimuth
    Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
    Hum Mol Genet 14:3595-603. 2005
  6. ncbi request reprint Pharmacogenomic assessment of carboxylesterases 1 and 2
    Sharon Marsh
    Department of Medicine, Washington University School of Medicine and the Siteman Cancer Center, St Louis, MO 63110, USA
    Genomics 84:661-8. 2004
  7. pmc Efficient high-throughput resequencing of genomic DNA
    Raymond D Miller
    Washington University, Division of Dermatology, St Louis, Missouri 63110, USA
    Genome Res 13:717-20. 2003
  8. ncbi request reprint Primer design for PCR and sequencing in high-throughput analysis of SNPs
    Ellen F Vieux
    Division of Dermatology, Washington University School of Medicine, St Louis, MO 63110, USA
    Biotechniques . 2002
  9. pmc Distribution of human SNPs and its effect on high-throughput genotyping
    Daniel C Koboldt
    Department of Genetics, Washington University, St Louis, Missouri, USA
    Hum Mutat 27:249-54. 2006
  10. ncbi request reprint Kinetic FP-TDI assay for SNP allele frequency determination
    Ming Xiao
    Washington University School of Medicine, St Louis, MO, USA
    Biotechniques 34:190-7. 2003

Detail Information

Publications54

  1. ncbi request reprint Approaches to allele frequency determination
    P 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...
  2. ncbi request reprint High-throughput genotyping assay approaches
    P 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...
  3. ncbi request reprint Methods for genotyping single nucleotide polymorphisms
    P 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...
  4. ncbi request reprint SNP genotyping with fluorescence polarization detection
    Pui 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...
  5. ncbi request reprint Polymorphism discovery in 51 chemotherapy pathway genes
    Robert 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...
  6. ncbi request reprint Pharmacogenomic assessment of carboxylesterases 1 and 2
    Sharon 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...
  7. pmc Efficient high-throughput resequencing of genomic DNA
    Raymond 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...
  8. ncbi request reprint Primer design for PCR and sequencing in high-throughput analysis of SNPs
    Ellen 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...
  9. pmc Distribution of human SNPs and its effect on high-throughput genotyping
    Daniel 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...
  10. ncbi request reprint Kinetic FP-TDI assay for SNP allele frequency determination
    Ming 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...
  11. ncbi request reprint Localization of PSORS1 to a haplotype block harboring HLA-C and distinct from corneodesmosin and HCR
    Cynthia 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...
  12. ncbi request reprint Novel immunoglobulin superfamily gene cluster, mapping to a region of human chromosome 17q25, linked to psoriasis susceptibility
    Rebecca 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...
  13. ncbi request reprint Homogeneous primer extension assay with fluorescence polarization detection
    Tony M Hsu
    Division of Dermatology, Washington University, St Louis, MO, USA
    Methods Mol Biol 212:177-87. 2003
  14. pmc High-density single-nucleotide polymorphism maps of the human genome
    Raymond D Miller
    Washington University, Division of Dermatology, St Louis, MO, USA
    Genomics 86:117-26. 2005
    ..High-density maps of high-quality, characterized SNPs produced by this project are freely available...
  15. ncbi request reprint Identification of NR1I2 genetic variation using resequencing
    Cristi 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...
  16. ncbi request reprint A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis
    Cynthia 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...
  17. pmc A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci
    Ying 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)...
  18. pmc Role of excess inorganic pyrophosphate in primer-extension genotyping assays
    Ming 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...
  19. pmc Single-molecule analysis for molecular haplotyping
    Pui 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...
  20. doi request reprint High-throughput genotyping with primer extension fluorescent polarization detection
    Pui 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...
  21. pmc Natural variation in four human collagen genes across an ethnically diverse population
    Ting 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...
  22. pmc A simple DNA stretching method for fluorescence imaging of single DNA molecules
    Ting 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...
  23. pmc Common beta-adrenergic receptor polymorphisms are not associated with risk of sudden cardiac death in patients with coronary artery disease
    Zian H Tseng
    Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, University of California, San Francisco, USA
    Heart Rhythm 5:814-21. 2008
    ....
  24. ncbi request reprint Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis
    Goncalo 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...
  25. pmc Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels
    David 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...
  26. pmc An apolipoprotein A-V gene SNP is associated with marked hypertriglyceridemia among Asian-American patients
    Clive 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...
  27. pmc SNPs meet CNVs in genome-wide association studies: HGV2007 meeting report
    Xavier Estivill
    Genes and Disease Program, Center for Genomic Regulation CRG UPF, Barcelona, Spain
    PLoS Genet 4:e1000068. 2008
  28. ncbi request reprint Arteriovenous malformation
    William L Young
    J Neurosurg 106:731-2; author reply 732-3. 2007
  29. ncbi request reprint Determination of haplotypes from single DNA molecules: a method for single-molecule barcoding
    Ming 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...
  30. pmc Gene-trapped mouse embryonic stem cell-derived cardiac myocytes and human genetics implicate AKAP10 in heart rhythm regulation
    Whittemore 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...
  31. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly 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...
  32. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  33. pmc Endothelial nitric oxide synthase polymorphism (-786T->C) and increased risk of angiographic vasospasm after aneurysmal subarachnoid hemorrhage
    Nerissa 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...
  34. ncbi request reprint Association of tumor necrosis factor-alpha-238G>A and apolipoprotein E2 polymorphisms with intracranial hemorrhage after brain arteriovenous malformation treatment
    Achal 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...
  35. pmc Genome-wide association studies getting more complicated but help is on the way
    Pui Yan Kwok
    Hum Genomics 2:341-2. 2006
  36. ncbi request reprint Adrenoceptor polymorphisms and the risk of cardiac injury and dysfunction after subarachnoid hemorrhage
    Jonathan 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...
  37. ncbi request reprint Apolipoprotein E epsilon 2 is associated with new hemorrhage risk in brain arteriovenous malformations
    Ludmila 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...
  38. ncbi request reprint Making 'random amplification' predictable in whole genome analysis
    Pui 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
    ....
  39. ncbi request reprint SNP discovery by direct DNA sequencing
    Pui Yan Kwok
    Cardiovascular Research Institute, Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
    Methods Mol Biol 212:71-84. 2003
  40. pmc DNA analysis by fluorescence quenching detection
    Ming 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...
  41. ncbi request reprint Detection of single nucleotide polymorphisms
    Pui 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...
  42. ncbi request reprint ADAM33 is not associated with asthma in Puerto Rican or Mexican populations
    Denise 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...
  43. ncbi request reprint Polymorphisms in genes involved in inflammatory and angiogenic pathways and the risk of hemorrhagic presentation of brain arteriovenous malformations
    Ludmila 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...
  44. ncbi request reprint Variations in human HM74 (GPR109B) and HM74A (GPR109A) niacin receptors
    Christian 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...
  45. ncbi request reprint Genetic admixture and asthma-related phenotypes in Mexican American and Puerto Rican asthmatics
    Keyan 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...
  46. ncbi request reprint Kinetic fluorescence-quenching detection assay for allele frequency estimation
    Ming 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...
  47. pmc Lack of support for the association between GAD2 polymorphisms and severe human obesity
    Michael M Swarbrick
    Diabetes Center, University of California, San Francisco, California, USA
    PLoS Biol 3:e315. 2005
    ....
  48. ncbi request reprint Polymorphisms in transforming growth factor-beta-related genes ALK1 and ENG are associated with sporadic brain arteriovenous malformations
    Ludmila 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...
  49. pmc Population structure, admixture, and aging-related phenotypes in African American adults: the Cardiovascular Health Study
    Alexander 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...
  50. ncbi request reprint Interleukin-6 involvement in brain arteriovenous malformations
    Yongmei Chen
    Center for Cerebrovascular Research, University of California at San Francisco, 1001 Potrero Avenue, San Francisco, CA, USA
    Ann Neurol 59:72-80. 2006
    ....
  51. ncbi request reprint Population stratification confounds genetic association studies among Latinos
    Shweta 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...
  52. ncbi request reprint 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 malformations
    Achal S Achrol
    Department of Anesthesia and Perioperative Care, Center for Cerebrovascular Research, University of California, San Francisco, California, USA
    Stroke 37:231-4. 2006
    ....
  53. ncbi request reprint 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...
  54. ncbi request reprint Paternal origins of complete hydatidiform moles proven by whole genome single-nucleotide polymorphism haplotyping
    Jian Bing Fan
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Genomics 79:58-62. 2002
    ....