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Table 1 Summary of studies on geneticsof human gene expression: Study characteristics

From: Gene expression endophenotypes: a novel approach for gene discovery in Alzheimer's disease

Reference Reference ID Organism Tissue Sample Size Samples Transcript Platform Genotyping Platform
Yan et al., 2002 [28] Human Lymphoblastoid cell lines (LCL) 96 Subjects from the CEPH families (17-37 subjects who were heterozygouse for any given gene) ABI Prism SNaPshot Multiplex Kit for 13 genes. SNPs for 13 genes.
Schadt et al., 2003 [29] Mouse Liver 111 F2 mice constructed from two standard inbred strains, C57BL/6J and DBA/2J 23,574 transcripts (Rosetta Inpharmatics Merck). >100 microsatellite markers.
   Z. mays (corn) Ear leaf tissue 76 An F3 cross constructed from standard inbred lines of Z. mays 24,473 transcripts (Rosetta Inpharmatics Merck). NA
   Human Lymphoblastoid cell lines (LCL) 56 Subjects from four CEPH families 24,479 transcripts (Rosetta Inpharmatics Merck). NA
Cheung et al., 2003 [30] Human Lymphoblastoid cell lines (LCL) 45 35 unrelated subjects from CEPH families vs. 1 reference pool of 10 subjects. 5 genes assessed in a larger sample size (49 unrelated CEPH subjects, 41 sibs from 5 CEPH families and 10 monozygotic twin pairs). 5000 random cDNA clones from IMAGE consortium. Not done.
Morley et al., 2004 [31] Human Lymphoblastoid cell lines (LCL) 234 94 unrelated grandparents from CEPH families and ~140 subjects from 14 large CEPH families. 8,500 transcripts (Analysis restricted to 3554 most variable expression phenotypes). 2,756 autosomal SNP markers (SNP Consortium).
Monks et al., 2004 [32] Human Lymphoblastoid cell lines (LCL) 167 subjects From 15 CEPH families 23,499 transcripts (25K human gene oligonucleotide microarray) 346 autosomal genetic markers.
Cheung et al., 2005 [33] Human Lymphoblastoid cell lines (LCL) 57 Unrelated CEPH subjects. 374 transcripts (subset of Morley et al. 2004); Affymetrix Human Genome Focus arrays. 770,394 SNPs.
Stranger et al., 2005 [34] Human Lymphoblastoid cell lines (LCL) 60 HapMap Unrelated Caucasian Subjects (CEU) 1,433 transcripts for 630 genes (Illumina BeadArray, custom). 753,712 SNPs
Stranger et al., 2007 (Nature Genetics) [35] Human Lymphoblastoid cell lines (LCL) 270 HapMap Subjects, 4 populations (30 Caucasian trios (CEU), 45 unrelated Chinese (CHB), 45 unrelated Japanese (JPT), and 30 Yoruba trios (YRI)). 14,456 transcripts for 13,643 genes (Illumina, Sentrix Human Whole Genome-6 Expression BeadChip version 1). >2.2 million SNPs per population.
Stranger et al., 2007 (Science) [36] Human Lymphoblastoid cell lines (LCL) 210 HapMap unrelated subjects, 4 populations (60 Caucasians (CEU), 45 Chinese (CHB), 45 Japanese (JPT), 60 Yoruban (YRI)). 14,925 transcripts for 14,072 genes Phase 1 HapMap SNPs and CNV data from comparative genomic hybridization (CGH) array of 26,574 clones.
Dixon et al., 2007 [37] Human Lymphoblastoid cell lines (LCL) 400 Affected and unaffected children from families with an asthma proband. 54,675 transcripts representing 20,599 genes (Affymetrix HG-U133 Plus 2.0 chip). 109,157 SNPs for 830 subjects (Illumina Sentrix Human-1 Genotyping BeadChip) and 299,116 SNPs for 378 subjects (Illumina Sentrix HumanHap300 BeadChip).
Goring et al., 2007 [38] Human Lymphocytes (not transformed cells) 1240 Multigenerational Mexican-American families from the San Antonio Family Heart Study (SAFHS). 19,648 transcripts for 18,519 genes (Illumina, Sentrix Human Whole Genome-6 Expression BeadChip version 1). 432 highly polymorphic microsatellite markers.
Emilsson et al., 2008 [39] Human Blood and adipose tissue 1,002 blood and 673 adipose cohorts. Icelandic Family Blood (IFB) cohort (N = 1,002) and the Icelandic Family Adipose (IFA) cohort (N = 673). 20,877 transcripts 1,732 microsatellite markers for linkage analysis and 317,503 SNPs for association analysis (150 unrelated subjects).
Schadt et al., 2008 [40] Human Liver 427 Unrelated subjects. 39,280 transcripts for 34,266 genes (Custom Agilent microarray). 782,476 unique SNPs (Affymetrix 500 K and Illumina 650Y)
Myers et al., 2007 [41] Human Brain 193 Human brain samples that are neuropathologically normal. 14,078 transcripts (Illumina HumanRefseq-8 Expression BeadChip). 366,140 SNPs (Affymetrix 500 K).
Webster et al., 2009 [42] Human Brain 176 cases and 188 controls. Human brain samples that are neuropathologically normal and with pathological Alzheimer's disease (AD). 8,650 transcripts (Illumina HumanRefseq-8 Expression BeadChip). 380,157 SNPs (Affymetrix 500 K).