Breast and Prostate Cancer and Hormone-Related Gene Variant Study
Gene Resequencing
Extensive resequencing is taking place on 75 candidate genes at three Genomics Centers:
- Centre d'Etude du Polymorphisme Humain
(CEPH)
For more information, contact Dr. Gilles Thomas - The Broad Institute of MIT and
Harvard
For more information, contact Dr. David Altshuler - NCI Core Genotyping Facility
For more information, contact Dr. Stephen Chanock
The division of labor is indicated in the table below. In each of the three laboratories, parallel activities are proceeding with both the resequencing of all 75 genes in the 190 cases and the identification of ht-SNPs, based on 733 unrelated subjects genotyped by different technologies. Common to all three centers is a common strategy for resequencing genes identified from the 190 cases of prostate and breast cancer.
List of 75 Genes Analyzed in the BPC3 Genomics Center
| Gene Name | Pathway | Description | Platform | Breast | Prostate |
|---|---|---|---|---|---|
| GHR | IGF | GROWTH HORMONE RECEPTOR | Illumina | x | x |
| GHRH | IGF | GROWTH HORMONE-RELEASING HORMONE | Illumina* | x | x |
| GHRHR | IGF | GROWTH HORMONE-RELEASING HORMONE RECEPTOR | Illumina* | x | x |
| IGF1 | IGF | INSULIN-LIKE GROWTH FACTOR I | Taqman | x | x |
| IGF1R | IGF | INSULIN-LIKE GROWTH FACTOR I RECEPTOR | Illumina | x | x |
| IGF2 | IGF | INSULIN-LIKE GROWTH FACTOR 2 | Illumina | x | x |
| IGF2R | IGF | INSULIN-LIKE GROWTH FACTOR II RECEPTOR | Illumina | x | x |
| IGFALS | IGF | IGFBP ACID-LABILE SUBUNIT | Illumina | x | x |
| IGFBP1 | IGF | INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN | Taqman | x | x |
| IGFBP2/5 | IGF | INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN | Illumina | x | x |
| IGFBP3 | IGF | INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN | Taqman | x | x |
| IGFBP4 | IGF | INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN | Illumina | x | x |
| IGFBP6 | IGF | INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN | Illumina | x | x |
| INSR | IGF | INSULIN RECEPTOR | Illumina | x | x |
| IRS1 | IGF | INSULIN RECEPTOR SUBSTRATE 1 | Illumina | x | x |
| IRS2 | IGF | INSULIN RECEPTOR SUBSTRATE 2 | Illumina | x | x |
| POU1F1 | IGF | POU DOMAIN, CLASS 1, TRANSCRIPTION FACTOR 1 | Illumina | x | x |
| SST | IGF | SOMATOSTATIN | Illumina | x | x |
| SSTR1 | IGF | SOMATOSTATIN RECEPTOR 1 | Illumina | x | x |
| SSTR2 | IGF | SOMATOSTATIN RECEPTOR 2 | Illumina | x | x |
| SSTR3 | IGF | SOMATOSTATIN RECEPTOR 3 | Illumina | x | x |
| SSTR4 | IGF | SOMATOSTATIN RECEPTOR 4 | Illumina | x | x |
| SSTR5 | IGF | SOMATOSTATIN RECEPTOR 5 | Illumina | x | x |
| IL6 | inflam (?) | INTERLEUKIN 6 | Illumina | x | x |
| PTGS2 | inflam (?) | PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 2 | Illumina | x | x |
| TLR4 | inflam (?) | TOLL-LIKE RECEPTOR | Taqman | x | x |
| PIK3AP1 | PIK | PHOSPHOINOSITIDE 3-KINASE ADAPTOR PROTEIN 1 | Illumina | x | x |
| PIK3C2A | PIK | PHOSPHATIDYLINOSITOL 3-KINASE, CLASS 2, ALPHA | Illumina | x | x |
| PIK3C2B | PIK | PHOSPHATIDYLINOSITOL 3-KINASE, CLASS 2, BETA | Illumina | x | x |
| PIK3CD | PIK | PHOSPHATIDYLINOSITOL 3-KINASE, CATALYTIC, DELTA | Illumina | x | x |
| PIK3R3 | PIK | PHOSPHATIDYLINOSITOL 3-KINASE, REGULATORY SUBUNIT 3 | Illumina | x | x |
| CASP8 | replication | CASPASE 8 | Illumina | x | x |
| CAT | replication | CATALASE | Illumina | x | x |
| DPF3 | replication | Illumina | x | x | |
| GPX1 | replication | GLUTATHIONE PEROXIDASE | Illumina | x | x |
| ICAM1 | replication | INTERCELLULAR ADHESION MOLECULE | x | x | |
| ICAM5 | replication | INTERCELLULAR ADHESION MOLECULE | Illumina | x | x |
| MC2R | replication | MELANOCORTIN 2 RECEPTOR | Illumina | x | x |
| MnSOD | replication | SUPEROXIDE DISMUTASE | Taqman | x | x |
| MPO | replication | MYELOPEROXIDASE | Taqman | x | x |
| ACTHR | steroid | ADRENOCORTICOTROPIC HORMONE RECEPTOR | Taqman | x | x |
| ACVR1 | steroid | ACTIVIN A RECEPTOR, TYPE I | Illumina | x | x |
| ACVR2 | steroid | ACTIVIN A RECEPTOR, TYPE II | Illumina | x | x |
| AKR1C3 | steroid | ALDO-KETO REDUCTASE FAMILY 1, MEMBER C3 | Illumina | x | x |
| AR | steroid | ANDROGEN RECEPTOR | Taqman | x | x |
| CGA | steroid | CHORIONIC GONADOTROPIN | Illumina | x | x |
| COMT | steroid | CATECHOL - O -METHYL TRANSFERASE | Taqman | x | x |
| CYP11A | steroid | Taqman | x | x | |
| CYP17 | steroid | Taqman | x | x | |
| CYP19 | steroid | Taqman | x | x | |
| CYP1A1 | steroid | Taqman | x | x | |
| CYP1A2 | steroid | Taqman | x | x | |
| CYP1B1 | steroid | Taqman | x | x | |
| CYP3A4 | steroid | Illumina | x | x | |
| ESR1 | steroid | ESTROGEN RECEPTOR ALPHA | Illumina | x | x |
| ESR2 | steroid | ESTROGEN RECEPTOR BETA | Taqman* | x | x |
| FSHB | steroid | FOLLICLE-STIMULATING HORMONE BETA UNIT | Taqman | x | x |
| FSHR | steroid | FOLLICLE-STIMULATING HORMONE RECEPTOR | Illumina | x | x |
| HSD17B1 | steroid | 17-BETA-HYDROXYSTEROID DEHYDROGENASE 1 | Taqman | x | x |
| HSD17B2 | steroid | 17-BETA-HYDROXYSTEROID DEHYDROGENASE 2 | Taqman | x | x |
| HSD17B3 | steroid | 17-BETA-HYDROXYSTEROID DEHYDROGENASE 3 | Illumina | x | x |
| HSD17B4 | steroid | 17-BETA-HYDROXYSTEROID DEHYDROGENASE 4 | Illumina | x | x |
| HSD3B1/2 | steroid | 3-BETA-HYDROXYSTEROID DEHYDROGENASE | Illumina | x | x |
| INHA | steroid | INHIBIN, ALPHA | Illumina | x | x |
| INHBA | steroid | INHIBIN, BETA A | Illumina | x | x |
| INHBB | steroid | INHIBIN, BETA B | Illumina | x | x |
| LHB | steroid | LUTEINIZING HORMONE, BETA | Illumina | x | x |
| LHCGR | steroid | LUTEINIZING HORMONE/CHORIOGONADOTROPIN RECEPTOR | Illumina | x | x |
| PGR | steroid | PROGESTERONE RECEPTOR | Illumina* | x | x |
| POMC | steroid | PROOPIOMELANOCORTIN | Illumina | x | x |
| PRL | steroid | PROLACTIN | Illumina | x | x |
| PRLR | steroid | PROLACTIN RECEPTOR | Illumina | x | x |
| SHBG | steroid | SEX HORMONE-BINDING GLOBULIN | Illumina | x | x |
| SRD5A1 | steroid | STEROID 5-ALPHA-REDUCTASE 1 | Illumina | x | x |
| SRD5A2 | steroid | STEROID 5-ALPHA-REDUCTASE 2 | Illumina | x | x |
| UGTB7/17 | steroid | URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 2, B7 | Illumina | x | x |
*Both Illumina and Taqman SNPs
