Biomedical Engineering Reference
In-Depth Information
22. Carlson, C.S., Eberle, M.A., Rieder, M.J.
et al
. (2004) Selecting a maximally informative set of
single-nucleotide polymorphisms for association analyses using linkage disequilibrium.
American
Journal of Human Genetics
,
74
, 106 -120.
23. Pritchard, J.K. and Przeworski, M. (2001) Linkage disequilibrium in humans: models and data.
American Journal of Human Genetics
,
69
, 1 - 14.
24. Moskvina, V. and O'Donovan, M.C. (2007) Detailed analysis of the relative power of direct
and indirect association studies and the implications for their interpretation.
Human Heredity
,
64
,
63 - 73.
25. Edlund, C.K., Lee, W.H., Li, D., Van Den Berg, D.J. and Conti, D.V. (2008) Snagger: a user-
friendly program for incorporating additional information for tagSNP selection.
BMC Bioinfor-
matics
,
9
, 174.
26. De Bakker, P.I., Yelensky, R., Pe'er, I.
et al
. (2005) Efficiency and power in genetic association
studies.
Nature Genetics
,
37
, 1217 -1223.
27. Johnson, A.D., Handsaker, R.E., Pulit, S.L.
et al
. (2008) SNAP: a web-based tool for identification
and annotation of proxy SNPs using HapMap.
Bioinformatics (Oxford, England)
,
24
, 2938 - 2939.
28. Li, C., Li, M., Long, J.R.
et al
. (2008) Evaluating cost efficiency of SNP chips in genome-wide
association studies.
Genetic Epidemiology
,
32
, 387 - 395.
29. Li, M., Li, C. and Guan, W. (2008) Evaluation of coverage variation of SNP chips for genome-wide
association studies.
European Journal of Human Genetics
,
16
, 635 - 643.
30. Saccone, S.F., Bierut, L.J., Chesler, E.J.
et al
. (2009) Supplementing high-density SNP microarrays
for additional coverage of disease-related genes: addiction as a paradigm.
PLoS One
,
4
, e5225.
31. Keating, B.J., Tischfield, S., Murray, S.S.
et al
. (2008) Concept, design and implementation of
a cardiovascular gene-centric 50 K SNP array for large-scale genomic association studies.
PLoS
ONE
,
3
, e3583.
32. Wigginton, J.E. and Abecasis, G.R. (2005) PEDSTATS: descriptive statistics, graphics and quality
assessment for gene mapping data.
Bioinformatics (Oxford, England)
,
21
, 3445 - 3447. Describes
PEDSTATS, a user-friendly program for performing quality control checks of both family-based
and unrelated samples.
33. Purcell, S., Neale, B., Todd-Brown, K.
et al
. (2007) PLINK: a tool set for whole-genome associa-
tion and population-based linkage analyses.
American Journal of Human Genetics
,
81
, 559 - 575.
Introduces and describes PLINK, an excellent and widely used software package for analysis of
genome-wide SNP data.
34. Suarez, B.K., Taylor, C., Bertelsen, S.
et al
. (2005) An analysis of identical single-nucleotide
polymorphisms genotyped by two different platforms.
BMC Genetics
,
6
(Suppl. 1), S152.
35. Pritchard, J.K., Stephens, M. and Donnelly, P. (2000) Inference of population structure using
multilocus genotype data.
Genetics
,
155
, 945 - 959.
36. Devlin, B. and Roeder, K. (1999) Genomic control for association studies.
Biometrics
,
55
,
997 - 1004.
37. Price, A.L., Patterson, N.J., Plenge, R.M.
et al
. (2006) Principal components analysis corrects for
stratification in genome-wide association studies.
Nature Genetics
,
38
, 904 - 909. The publication
for EIGENSTRAT, an excellent and popular program for testing and correcting for population
stratification.
38. Tian, C., Hinds, D.A., Shigeta, R.
et al
. (2007) A genomewide single-nucleotide -polymorphism
panel for Mexican American admixture mapping.
American Journal of Human Genetics
,
80
,
1014 -1023.