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). |