My complex disease trait mapping, genome mapping, linkage analysis journal watch - year 2003 [ this week | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 ]


General
Linkage & whole genome mapping
Sibpair
Linkage disequilibrium
Quantitative Trait Loci (QTL)
Theoretical development
Software
Database
Genetic map development
 

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General
  1. Goldstein DB, Ahmadi KR, Weale ME, Wood NW. Genome scans and candidate gene approaches in the study of common diseases and variable drug responses. Trends Genet. 2003 Nov;19(11):615-22.  [PubMed]
  2. Zhang J, Rowe WL, Clark AG, Buetow KH. Genomewide Distribution of High-Frequency, Completely Mismatching SNP Haplotype Pairs Observed To Be Common across Human Populations. Am J Hum Genet. 2003 Nov;73(6):1073-81. [PubMed]
  3. Rahman P, Jones A, Curtis J, Bartlett S, Peddle L, Fernandez BA, Freimer NB. The Newfoundland Population: A Unique Resource for Genetic Investigation of Complex Diseases. Hum Mol Genet. 2003 Oct 15;12 Suppl 2:R167-72. [PubMed]
  4. Kraft P, Horvath S. The genetics of gene expression and gene mapping. Trends Biotechnol. 2003 Sep;21(9):377-8. [PubMed]
  5. Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet. 2003 Mar;33 Suppl:228-37. [PubMed]
Linkage & whole genome mapping
  1. Moreno C, Dumas P, Kaldunski ML, Tonellato PJ, Greene AS, Roman RJ, Cheng Q, Wang Z, Jacob HJ, Cowley Jr AW. Genomic map of cardiovascular phenotypes of hypertension in female Dahl S rats. Physiol Genomics. 2003 Nov 11;15(3):243-57. [PubMed]
  2. De Jong MM, Nolte IM, De Vries EG, Schaapveld M, Kleibeuker JH, Oosterom E, Oosterwijk JC, Van Der Hout AH, Van Der Steege G, Bruinenberg M, Boezen HM, Te Meerman GJ, Van Der Graaf WT. The HLA class III subregion is responsible for an increased breast cancer risk. Hum Mol Genet. 2003 Sep 15;12(18):2311-9. [PubMed]
  3. Cardon LR, Abecasis GR. Using haplotype blocks to map human complex trait loci. Trends Genet 2003 Mar; 19:135-140. [PubMed]
  4. Marlow AJ, Fisher SE, Francks C, MacPhie IL, Cherny SS, Richardson AJ, Talcott JB, Stein JF, Monaco AP, Cardon LR. Use of multivariate linkage analysis for dissection of a complex cognitive trait. Am J Hum Genet. 2003 Mar;72(3):561-70. [PubMed]
  5. Blacker D, Bertram L, Saunders AJ, Moscarillo TJ, Albert MS, Wiener H, Perry RT, Collins JS, Harrell LE, Go RC, Mahoney A, Beaty T, Fallin MD, Avramopoulos D, Chase GA, Folstein MF, McInnis MG, Bassett SS, Doheny KJ, Pugh EW, Tanzi RE. Results of a high-resolution genome screen of 437 Alzheimer's Disease families. Hum Mol Genet. 2003 Jan 1;12(1):23-32. [PubMed]
  6. Park YG, Clifford R, Buetow KH, Hunter KW. Multiple cross and inbred strain haplotype mapping of complex-trait candidate genes. Genome Res. 2003 Jan;13(1):118-21. [PubMed]

Sibpair
  1. Williams NM, Norton N, Williams H, Ekholm B, Hamshere ML, Lindblom Y, Chowdari KV, Cardno AG, Zammit S, Jones LA, Murphy KC, Sanders RD, McCarthy G, Gray MY, Jones G, Holmans P, Nimgaonkar V, Adolfson R, Osby U, Terenius L, Sedvall G, O'Donovan MC, Owen MJ. A Systematic Genomewide Linkage Study in 353 Sib Pairs with Schizophrenia. Am J Hum Genet. 2003 Dec;73(6):1355-67. [PubMed]
Linkage disequilibrium
  1. Wall JD, Pritchard JK. Assessing the Performance of the Haplotype Block Model of Linkage Disequilibrium. Am J Hum Genet. 2003 Sep;73(3):502-15. [PubMed]
  2. Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet. 2003 Aug;4(8):587-97. [PubMed]
  3. Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E. Linkage Disequilibrium and Inference of Ancestral Recombination in 538 Single-Nucleotide Polymorphism Clusters across the Human Genome. Am J Hum Genet. 2003 Aug;73(2):285-300. [PubMed]
  4. Meng Z, Zaykin DV, Xu CF, Wagner M, Ehm MG. Selection of Genetic Markers for Association Analyses, Using Linkage Disequilibrium and Haplotypes. Am J Hum Genet. 2003 Jul;73(1):115-30. [PubMed]
  5. Cheng R, Ma JZ, Wright FA, Lin S, Gao X, Wang D, Elston RC, Li MD. Nonparametric Disequilibrium Mapping of Functional Sites Using Haplotypes of Multiple Tightly Linked Single-Nucleotide Polymorphism Markers. Genetics 2003 Jul; 164: 1175-1187. [PubMed]
  6. Clark AG. Finding genes underlying risk of complex disease by linkage disequilibrium mapping. Curr Opin Genet Dev. 2003 Jun;13(3):296-302. [PubMed]
  7. Sabatti C, Service S, Freimer N. False discovery rate in linkage and association genome screens for complex disorders. Genetics. 2003 Jun;164(2):829-33. [PubMed]
  8. Twells RC, Mein CA, Phillips MS, Hess JF, Veijola R, Gilbey M, Bright M, Metzker M, Lie BA, Kingsnorth A, Gregory E, Nakagawa Y, Snook H, Wang WY, Masters J, Johnson G, Eaves I, Howson JM, Clayton D, Cordell HJ, Nutland S, Rance H, Carr P, Todd JA. Haplotype Structure, LD Blocks, and Uneven Recombination Within the LRP5 Gene. Genome Res. 2003 May;13(5):845-55. [PubMed]
  9. Fan R, Knapp M. Genome association studies of complex diseases by case-control designs. Am J Hum Genet. 2003 Apr;72(4):850-68. [PubMed]
  10. Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglyak L, Nickerson DA. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet. 2003 Apr;33(4):518-21. [PubMed][web supplement]
  11. Lou XY, Casella G, Littell RC, Yang MC, Johnson JA, Wu R. A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait Loci with epistasis. Genetics. 2003 Apr;163(4):1533-48. [PubMed]
  12. Ito T, Chiku S, Inoue E, Tomita M, Morisaki T, Morisaki H, Kamatani N. Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am J Hum Genet. 2003 Feb;72(2):384-98. [PubMed]
  13. Varilo T, Paunio T, Parker A, Perola M, Meyer J, Terwilliger JD, Peltonen L. The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum Mol Genet. 2003 Jan 1;12(1):51-59. [PubMed]
Quantitative Trait Loci (QTL)
  1. Members of the Complex Trait Consortium. THE NATURE AND IDENTIFICATION OF QUANTITATIVE TRAIT LOCI: A COMMUNITY'S VIEW. Nat Rev Genet. 2003 Nov; [PubMed]
  2. Yi N, Xu S, Allison DB. Bayesian model choice and search strategies for mapping interacting quantitative trait Loci. Genetics. 2003 Oct;165(2):867-83. [PubMed]
  3. Lin M, Lou XY, Chang M, Wu R. A General Statistical Framework for Mapping Quantitative Trait Loci in Nonmodel Systems. Issue for characterizing linkage phases. Genetics. 2003 Oct;165(2):901-13. [PubMed]
  4. T Cuenco K, Szatkiewicz JP, Feingold E. Recent Advances in Human Quantitative-Trait-Locus Mapping: Comparison of Methods for Selected Sibling Pairs.  Am J Hum Genet. 2003 Oct;73(4):863-73. [PubMed]
  5. Szatkiewicz JP, T Cuenco K, Feingold E. Recent Advances in Human Quantitative-Trait-Locus Mapping: Comparison of Methods for Discordant Sibling Pairs. Am J Hum Genet. 2003 Oct;73(4):874-85. [PubMed]
  6. Shete S, Zhou X, Amos CI. Genomic imprinting and linkage test for quantitative-trait Loci in extended pedigrees. Am J Hum Genet. 2003 Oct;73(4):933-8. [PubMed]
  7. Ronin Y, Korol A, Shtemberg M, Nevo E, Soller M. High-resolution mapping of quantitative trait Loci by selective recombinant genotyping. Genetics. 2003 Aug;164(4):1657-66. [PubMed]
  8. Perez-Enciso M, Toro MA, Tenenhaus M, Gianola D. Combining Gene Expression and Molecular Marker Information for Mapping Complex Trait Genes. A simulation study. Genetics. 2003 Aug;164(4):1597-606. [PubMed]
  9. Lan H, Stoehr JP, Nadler ST, Schueler KL, Yandell BS, Attie AD. Dimension reduction for mapping mRNA abundance as quantitative traits. Genetics. 2003 Aug;164(4):1607-14. [PubMed]
  10. Wang X, Le Roy I, Nicodeme E, Li R, Wagner R, Petros C, Churchill GA, Harris S, Darvasi A, Kirilovsky J, Roubertoux PL, Paige B. Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci. Genome Res. 2003 Jul;13(7):1654-64. [PubMed][pdf][web supplement]
  11. Yi N, George V, Allison DB. Stochastic Search Variable Selection for Identifying Multiple Quantitative Trait Loci. Genetics 2003 Jul; 164: 1129-1138. [PubMed]
  12. Broman KW, Wu H, Sen S, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003 May 1;19(7):889-90. [PubMed]
  13. Broman KW. Mapping quantitative trait Loci in the case of a spike in the phenotype distribution. Genetics. 2003 Mar;163(3):1169-75. [PubMed]
  14. Lund MS, Sorensen P, Guldbrandtsen B, Sorensen DA. Multitrait fine mapping of quantitative trait Loci using combined linkage disequilibria and linkage analysis. Genetics. 2003 Jan;163(1):405-10. [PubMed]

Theoretical development
  1. Wang WY, Todd JA. The usefulness of different density SNP maps for disease association studies of common variants. Hum Mol Genet. 2003 Dec 1;12(23):3145-9. [PubMed]
  2. Tishkoff SA, Verrelli BC. Role of evolutionary history on haplotype block structure in the human genome: implications for disease mapping. Curr Opin Genet Dev. 2003 Dec;13(6):569-75. [PubMed]
  3. Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003 Dec;73(6):1402-22. [PubMed]
  4. Epstein MP, Satten GA. Inference on Haplotype Effects in Case-Control Studies Using Unphased Genotype Data. Am J Hum Genet. 2003 Dec;73(6):1316-29. [PubMed]
  5. Molitor J, Marjoram P, Thomas D. Fine-Scale Mapping of Disease Genes with Multiple Mutations via Spatial Clustering Techniques. Am J Hum Genet. 2003 Dec;73(6):1368-84.  [PubMed]
  6. Martin ER, Bass MP, Hauser ER, Kaplan NL. Accounting for Linkage in Family-Based Tests of Association with Missing Parental Genotypes. Am J Hum Genet. 2003 Nov;73(6):1016-26. [PubMed]
  7. Stephens M, Donnelly P. A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet. 2003 Nov;73(6):1162-9. [PubMed]
  8. Turner FS, Clutterbuck DR, Semple CA. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol. 2003;4(11):R75. [PubMed]
  9. Yi N, Xu S, Allison DB. Bayesian model choice and search strategies for mapping interacting quantitative trait Loci. Genetics. 2003 Oct;165(2):867-83. [PubMed]
  10. Lin M, Lou XY, Chang M, Wu R. A General Statistical Framework for Mapping Quantitative Trait Loci in Nonmodel Systems. Issue for characterizing linkage phases. Genetics. 2003 Oct;165(2):901-13. [PubMed]
  11. Wall JD, Pritchard JK. Assessing the Performance of the Haplotype Block Model of Linkage Disequilibrium. Am J Hum Genet. 2003 Sep;73(3):502-15. [PubMed]
  12. Zhang S, Sha Q, Chen HS, Dong J, Jiang R. Transmission/Disequilibrium Test Based on Haplotype Sharing for Tightly Linked Markers. Am J Hum Genet. 2003 Sep;73(3):566-79. [PubMed]
  13. Tahri-Daizadeh N, Tregouet DA, Nicaud V, Manuel N, Cambien F, Tiret L. Automated detection of informative combined effects in genetic association studies of complex traits. Genome Res. 2003 Aug;13(8):1952-60. [PubMed][pdf]
  14. Huang J, Bhandarkar SM. A comparison of physical mapping algorithms based on the maximum likelihood model. Bioinformatics. 2003 Jul 22;19(11):1303-10. [PubMed]
  15. Arnheim N, Calabrese P, Nordborg M. Hot and Cold Spots of Recombination in the Human Genome: the Reason We Should Find Them and How This Can Be Achieved. Am J Hum Genet 2003 Jul; [PubMed]
  16. Mannila H, Koivisto M, Perola M, Varilo T, Hennah W, Ekelund J, Lukk M, Peltonen L, Ukkonen E. Minimum Description Length Block Finder, a Method to Identify Haplotype Blocks and to Compare the Strength of Block Boundaries. Am J Hum Genet 2003 Jul; [PubMed]
  17. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM. Control of Confounding of Genetic Associations in Stratified Populations. Am J Hum Genet 2003 Jun; [PubMed]
  18. Service SK, Sandkuijl LA, Freimer NB. Cost-Effective Designs for Linkage Disequilibrium Mapping of Complex Traits. Am J Hum Genet. 2003 May;72(5):1213-20. [PubMed]
  19. Kraft P, Schadt E, Aten J, Horvath S. A Family-Based Test for Correlation between Gene Expression and Trait Values. Am J Hum Genet 2003 May;72(5):1323-30 [PubMed]
  20. Zhao LP, Li SS, Khalid N. A Method for the Assessment of Disease Associations with Single-Nucleotide Polymorphism Haplotypes and Environmental Variables in Case-Control Studies. Am J Hum Genet. 2003 May;72(5):1231-50. [PubMed]
  21. Law B, Buckleton JS, Triggs CM, Weir BS. Effects of population structure and admixture on exact tests for association between Loci. Genetics. 2003 May;164(1):381-7. [PubMed]
  22. Yang Q, Xu X, Laird N. Power evaluations for family-based tests of association with incomplete parental genotypes. Genetics. 2003 May;164(1):399-406. [PubMed]
  23. Wiuf C, Posada D. A coalescent model of recombination hotspots. Genetics. 2003 May;164(1):407-17. [PubMed]
  24. Tzeng JY, Devlin B, Wasserman L, Roeder K. On the Identification of Disease Mutations by the Analysis of Haplotype Similarity and Goodness of Fit. Am J Hum Genet 2003 Apr;72(4):891-902 [PubMed]
  25. Cardon LR, Palmer LJ. Population stratification and spurious allelic association. Lancet. 2003 Feb 15;361(9357):598-604. [PubMed]
  26. Conti DV, Witte JS. Hierarchical modeling of linkage disequilibrum: genetic structure and spatial relations. Am J Hum Genet. 2003 Feb;72(2):351-63. [PubMed]
  27. Ke X, Cardon LR. Efficient selective screening of haplotype tag SNPs. Bioinformatics. 2003 Jan;19(2):287-8. [PubMed]
  28. Posada D, Wiuf C. Simulating haplotype blocks in the human genome. Bioinformatics. 2003 Jan;19(2):289-90. [PubMed]
  29. Schlotterer C. Hitchhiking mapping - functional genomics from the population genetics perspective. Trends Genet. 2003 Jan;19(1):32-8. [PubMed]

Software
  1. Harris M, Martin JM, Peden JF, Rawlings CJ. SNP cherry picker: maximizing the chance of finding an association with a disease SNP. Bioinformatics. 2003 Nov 1;19(16):2141-3. [PubMed]
  2. Ding K, Zhou K, He F, Shen Y. LDA—a java-based linkage disequilibrium analyzer. Bioinformatics. 2003 Nov 1;19(16):2147-2148. [PubMed]
  3. Purcell S, Cherny SS, Sham PC. Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics. 2003 Jan;19(1):149-150. [PubMed]

Database

Nucleic Acid Research January 1, 2003 issue - The Molecular Biology Database Collection - The link to the complete issue

Genetic map development

  1. Ren C, Lee MK, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang HB. A BAC-Based Physical Map of the Chicken Genome. Genome Res. 2003 Dec; 13: 2754-2758. [PubMed]
  2. Mester D, Ronin Y, Minkov D, Nevo E, Korol A. Constructing large-scale genetic maps using an evolutionary strategy algorithm. Genetics. 2003 Dec; 165(4): 2269-82.  [PubMed]
  3. Zhou S, Kvikstad E, Kile A, Severin J, Forrest D, Runnheim R, Churas C, Hickman JW, Mackenzie C, Choudhary M, Donohue T, Kaplan S, Schwartz DC.    Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly. Genome Res. 2003 Sep;13(9):2142-51. [PubMed][pdf]
  4. Matise TC, Sachidanandam R, Clark AG, Kruglyak L, Wijsman E, Kakol J, Buyske S, Chui B, Cohen P, Toma Cd C, Ehm M, Glanowski S, He C, Heil J, Markianos K, McMullen I, Pericak-Vance MA, Silbergleit A, Stein L, Wagner M, Wilson AF, Winick JD, Winn-Deen ES, Yamashiro CT, Cann HM, Lai E, Holden AL. A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet. 2003 Aug;73(2):271-84. [PubMed]
  5. Collins JR, Stephens RM, Gold B, Long B, Dean M, Burt SK. An exhaustive DNA micro-satellite map of the human genome using high performance computing. Genomics. 2003 Jul;82(1):10-9. [PubMed]
  6. Chowdhary BP, Raudsepp T, Kata SR, Goh G, Millon LV, Allan V, Piumi F, Guerin G, Swinburne J, Binns M, Lear TL, Mickelson J, Murray J, Antczak DF, Womack JE, Skow LC. The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res. 2003 Apr;13(4):742-51. [PubMed][web supplement]
  7. Rowe LB, Barter ME, Kelmenson JA, Eppig JT. The comprehensive mouse radiation hybrid map densely cross-referenced to the recombination map: a tool to support the sequence assemblies. Genome Res. 2003 Jan;13(1):122-33. [PubMed]
last updated: 25 Jan 2004
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