Merging microsatellite data: Enhanced methodology and software to combine genotype data for linkage and association analysis

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Presson, Angela P ^a   Sobel, Eric M ^b   Pajukanta, Paivi ^b   Plaisier, Christopher ^b   Weeks, Daniel E ^c,d   Åberg, Karolina ^d   Papp, Jeanette C ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

^d UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION ANALYSIS; EXPERIMENTAL PROTOCOLS; GENETIC ANALYSIS; INDEPENDENT ANALYSIS; MICROSATELLITE DATA; MULTIPLE DATA SETS; STATISTICAL MODELING; STATISTICAL POWER;

ALIGNMENT; DNA SEQUENCES; FINITE DIFFERENCE METHOD; FORESTRY; GENES; MERGING;

QUALITY CONTROL;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DYSLIPIDEMIA; GENE FREQUENCY; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENOTYPE; HUMAN; INFORMATION PROCESSING; MICROSATELLITE MARKER; PEDIGREE ANALYSIS; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; BIOLOGY; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; TECHNIQUE;

MICROSATELLITE DNA;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENOTYPE; LINKAGE (GENETICS); METHODS; MICROSATELLITE REPEATS; MODELS, STATISTICAL; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 49649122096     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-317     Document Type: Article

References (15)

1. Ioannidis JP Genetic associations: False or true? Trends Mol Med 2003, 9(4):135-8 [1471-4914 (Print) Journal Article Review] 10.1016/ S1471-4914(03)00030-3 12727138
2. Burgner D Jamieson SE Blackwell JM Genetic susceptibility to infectious diseases: Big is beautiful, but will bigger be even better? Lancet Infect Dis 2006, 6(10):653-63 [1473-3099 (Print) Journal Article Research Support, Non-U.S. Gov't Review] 2330096 17008174 10.1016/ S1473-3099(06)70601-6
3. Freimer N Sabatti C The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology Nat Genet 2004, 36(10):1045-51 [1061-4036 (Print) Journal Article Review] 10.1038/ng1433 15454942
4. Presson AP Sobel E Lange K Papp JC Merging microsatellite data J Comput Biol 2006, 13(6):1131-47 [1066-5277 (Print) Journal Article] 10.1089/ cmb.2006.13.1131 16901233
5. Chen GK Slaten E Ophoff RA Lange K Accommodating chromosome inversions in linkage analysis Am J Hum Genet 2006, 79(2):238-51 [Chen, Gary K Slaten, Erin Ophoff, Roel A Lange, Kenneth GM068875/GM/United States NIGMS GM53275/GM/United States NIGMS MH59490/MH/United States NIMH T32 HG02536/HG/United States NHGRI Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't United States American journal of human genetics Am J Hum Genet. 2006 Aug;79(2):238-51. Epub 2006 Jun 6.] 1559487 16826515 10.1086/505540
6. Dorr DA Rice JP Armstrong C Reich T Blehar M A meta-analysis of chromosome 18 linkage data for bipolar illness Genet Epidemiol 1997, 14(6):617-22 [Dorr, D A Rice, J P Armstrong, C Reich, T Blehar, M MH31302/MH/United States NIMH MH37685/MH/United States NIMH Meta-Analysis Research Support, U.S. Gov't, P.H.S. United states Genetic epidemiology Genet Epidemiol. 1997;14(6):617-22.] 10.1002/ (SICI)1098-2272(1997)14:6<617::AID-GEPI11>3.0.CO;2-T 9433552
7. Weeks DE Conley YP Ferrell RE Mah TS Gorin MB A tale of two genotypes: consistency between two high-throughput genotyping centers Genome Res 2002, 12(3):430-5 [1088-9051 (Print) Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.] 155285 11875031 10.1101/gr.211502
8. Idury RM Cardon LR A simple method for automated allele binning in microsatellite markers Genome Res 1997, 7(11):1104-9 [Idury, R M Cardon, L R United states Genome research Genome Res. 1997 Nov;7(11):1104-9.] 310687 9371746
9. Lange K Cantor R Horvath S Perola M Sabatti C Sinsheimer J Sobel E Mendel version 4.0: A complete package for the exact genetic analysis of discrete traits in pedigree and population data sets Am J Hum Genet 2001:69 supplement A1886
10. Kruglyak L Daly MJ Reeve-Daly MP Lander ES Parametric and nonparametric linkage analysis: A unified multipoint approach Am J Hum Genet 1996, 58(6):1347-63 [0002-9297 (Print) Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.] 1915045 8651312
11. Abecasis GR Cherny SS Cookson WO Cardon LR Merlin-rapid analysis of dense genetic maps using sparse gene flow trees Nat Genet 2002, 30:97-101 [1061-4036 (Print) Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.] 10.1038/ ng786 11731797
12. Lathrop GM Lalouel JM Julier C Ott J Strategies for multilocus linkage analysis in humans Proc Natl Acad Sci USA 1984, 81(11):3443-6 [0027-8424 (Print) Journal Article] 345524 6587361 10.1073/pnas.81.11.3443
13. Sheffield VC Weber JL Buetow KH Murray JC Even DA Wiles K Gastier JM Pulido JC Yandava C Sunden SL A collection of tri- and tetranucleotide repeat markers used to generate high quality, high resolution human genome-wide linkage maps Hum Mol Genet 1995, 4(10):1837-44 [Sheffield, V C Weber, J L Buetow, K H Murray, J C Even, D A Wiles, K Gastier, J M Pulido, J C Yandava, C Sunden, S L P50HG00835/HG/United States NHGRI Research Support, U.S. Gov't, P.H.S. England Human molecular genetics Hum Mol Genet. 1995 Oct;4(10):1837-44.] 10.1093/hmg/4.10.1837 8595404
14. Pajukanta P Allayee H Krass KL Kuraishy A Soro A Lilja HE Mar R Taskinen MR Nuotio I Laakso M Rotter JI de Bruin TW Cantor RM Lusis AJ Peltonen L Combined analysis of genome scans of dutch and finnish families reveals a susceptibility locus for high-density lipoprotein cholesterol on chromosome 16q Am J Hum Genet 2003, 72(4):903-17 [Pajukanta, Paivi Allayee, Hooman Krass, Kelly L Kuraishy, Ali Soro, Aino Lilja, Heidi E Mar, Rebecca Taskinen, Marja-Riitta Nuotio, Ilpo Laakso, Markku Rotter, Jerome I de Bruin, Tjerk W A Cantor, Rita M Lusis, Aldons J Peltonen, Leena 5-t32-gm08243-15/gm/nigms Hl-28481/hl/nhlbi Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. United States American journal of human genetics Am J Hum Genet. 2003 Apr;72(4):903-17. Epub 2003 Mar 12.] 1180353 12638083 10.1086/374177
15. Neyman J Pearson E On the Problem of the Most Efficient Tests of Statistical Hypotheses Philosophical Transactions of the Royal Society of London. Series A, Containing Papers of a Mathematical or Physical Character 1933, 231:289-337 10.1098/rsta.1933.0009