Dataset: Genomic Grade Index (GGI): Feasibility in routine practice and impact on treatment decisions in early breast cancer
Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this...
Genomic Grade Index (GGI) is a 97-gene signature that improves histologic grade (HG) classification in invasive breast carcinoma. In this prospective study we sought to evaluate the feasibility of performing GGI in routine clinical practice and its impact on treatment recommendations. Patients with pT1pT2 or operable pT3, N0-3 invasive breast carcinoma were recruited from 8 centers in Belgium. Fresh surgical samples were sent at room temperature in the MapQuant Dx™ PathKit for centralized genomic analysis. Genomic profiles were determined using Affymetrix U133 Plus 2.0 and GGI calculated using the MapQuant Dx™ protocol, which defines tumors as low or high Genomic Grade (GG-1 and GG-3 respectively). 180 pts were recruited and 155 were eligible. The MapQuant test was performed in 142 cases and GGI was obtained in 78% of cases (n=111). Reasons for failures were 15 samples with <30% of invasive tumor cells (11%), 15 with insufficient RNA quality (10%), and 1 failed hybridization (<1%). For tumors with an available representative sample (≥ 30% inv. tumor cells) (n=127), the success rate was 87.5 %. GGI reclassified 69% of the 54 HG2 tumors as GG-1 (54%) or GG-3 (46%). Changes in treatment recommendations occurred mainly in the subset of HG2 tumors reclassified into GG-3, with increased use of chemotherapy in this subset. The use of GGI is feasible in routine clinical practice and impacts treatment decisions in early-stage breast cancer. Total RNA was extracted from fresh tumor tissues comprising ≥30% invasive tumor cells and hybridized on Affymetrix microarrays if the RIN was ≥ 7.
- Species:
- human
- Samples:
- 111
- Source:
- E-GEOD-43365
- Updated:
- Dec.12, 2014
- Registered:
- Jul.12, 2014
Factors:
(via ArrayExpress)
| Sample | PR | MENOP | CENTRE | COMORB | GRADE HISTO | AGE | HIST | GG | SIZE MM | HER2 | NODES | GGI | ER |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GSM1061142 | 1 | postmenopausal | 1 | average for age | 2 | 80 | lobular | equivocal | 15 | 0 | 0 | -0.3 | 1 |
| GSM106114 | 1 | postmenopausal | 1 | minor | 1 | 75 | ductal | equivocal | 10 | 0 | 0 | 0.2 | 1 |
| GSM1061140 | 0 | premenopausal | 1 | minor | 3 | 42 | ductal | 3 | 17 | 0 | 0 | 2 | 1 |
| GSM1061139 | 1 | postmenopausal | 1 | minor | 1 | 51 | ductal | 1 | 11 | 0 | 0 | -1.5 | 1 |
| GSM1061138 | 1 | NA | 1 | minor | 3 | 41 | ductal | 3 | 16 | 1 | 0 | 0.6 | 1 |
| GSM1061137 | 0 | premenopausal | 6 | perfect health | 3 | 48 | ductal | 3 | 28 | 0 | 0 | 3.1 | 1 |
| GSM1061136 | 1 | postmenopausal | 6 | perfect health | 3 | 60 | ductal | 3 | 8 | 1 | 0 | 0.5 | 1 |
| GSM1061135 | 0 | NA | 6 | perfect health | 1 | 56 | ductal | 1 | 12 | 0 | 0 | -0.6 | 1 |
| GSM1061134 | 0 | postmenopausal | 6 | major problems | 2 | 78 | ductal | 3 | 45 | 0 | 1 | 0.4 | 1 |
| GSM1061133 | 1 | premenopausal | 6 | perfect health | 2 | 43 | ductal | 1 | 12 | 0 | 0 | -0.7 | 1 |
| GSM1061132 | 1 | NA | 6 | perfect health | 2 | 69 | ductal | 3 | 42 | 0 | 2 | 1.4 | 1 |
| GSM106113 | 0 | NA | 6 | perfect health | 2 | 53 | ductal | 1 | 18 | 0 | 0 | -0.6 | 1 |
| GSM1061130 | 1 | postmenopausal | 6 | perfect health | 3 | 54 | lobular | 1 | 32 | 1 | 0 | -0.7 | 1 |
| GSM1061129 | 1 | NA | 6 | major problems | 2 | 63 | ductal | 1 | 35 | 0 | 0 | -1.1 | 1 |
| GSM1061128 | 0 | premenopausal | 6 | perfect health | 3 | 38 | ductal | 3 | 17 | 0 | 0 | 2.4 | 0 |
| GSM1061127 | 1 | postmenopausal | 6 | major problems | 3 | 70 | ductal | 3 | 45 | 0 | 1 | 1.6 | 1 |
| GSM1061126 | 1 | postmenopausal | 3 | minor | 2 | 53 | lobular | 1 | 8 | 0 | 0 | -1.2 | 1 |
| GSM1061125 | 1 | postmenopausal | 3 | minor | 2 | 62 | ductal | equivocal | 15 | 0 | 0 | -0.3 | 1 |
| GSM1061124 | 1 | postmenopausal | 3 | minor | 2 | 58 | ductal | equivocal | 18 | 0 | 1 | 0.1 | 1 |
| GSM1061123 | 1 | postmenopausal | 3 | minor | 1 | 51 | ductal | 1 | 12 | 0 | 0 | -1 | 1 |
| GSM1061122 | 1 | premenopausal | 1 | minor | 2 | 43 | ductal | equivocal | 13 | 0 | 0 | -0.1 | 1 |
| GSM106112 | 1 | postmenopausal | 6 | minor | 1 | 56 | lobular | 1 | 20 | 0 | 0 | -1 | 1 |
| GSM1061120 | 0 | premenopausal | 6 | perfect health | 3 | 45 | ductal | 3 | 13 | 0 | 1 | 1.2 | 1 |
| GSM1061119 | 1 | postmenopausal | 6 | major problems | 2 | 64 | ductal | 1 | 6 | 0 | 0 | -1.9 | 1 |
| GSM1061118 | 0 | postmenopausal | 6 | major problems | 3 | 87 | ductal | 3 | 45 | 1 | 0 | 1.9 | 0 |
| GSM1061117 | 1 | NA | 6 | minor | 2 | 51 | ductal | 1 | 13 | 0 | 1 | -0.4 | 1 |
| GSM1061116 | 1 | postmenopausal | 6 | minor | 2 | 67 | lobular | 1 | 30 | 0 | 0 | -2.3 | 1 |
| GSM1061115 | 1 | postmenopausal | 6 | average for age | 1 | 84 | ductal | 1 | 13 | 0 | 0 | -0.8 | 1 |
| GSM1061114 | 0 | postmenopausal | 9 | perfect health | 2 | 56 | ductal | 3 | 9 | 0 | 0 | 0.8 | 0 |
| GSM1061113 | 0 | premenopausal | 9 | perfect health | 3 | 47 | ductal | 3 | 33 | 0 | 0 | 3.3 | 0 |
| GSM1061112 | 1 | postmenopausal | 9 | perfect health | 1 | 78 | ductal | 1 | 17 | 0 | 0 | -0.5 | 1 |
| GSM106 | 0 | postmenopausal | 6 | NA | 3 | 76 | ductal | 3 | 30 | 1 | 2 | 1.6 | 0 |
| GSM1061110 | 1 | NA | 6 | major problems | 2 | 53 | ductal | equivocal | 15 | 0 | 0 | -0.1 | 1 |
| GSM1061109 | 1 | premenopausal | 6 | major problems | 1 | 52 | lobular | 1 | 12 | 0 | 0 | -2.3 | 1 |
| GSM1061108 | 1 | NA | 6 | minor | 2 | 47 | ductal | 1 | 16 | 0 | 0 | -1.5 | 1 |
| GSM1061107 | 1 | premenopausal | 6 | major problems | 1 | 49 | ductal | 3 | 15 | 0 | 0 | 1 | 1 |
| GSM1061106 | 1 | NA | 6 | perfect health | 2 | 58 | ductal | 3 | 15 | NA | 0 | 0.7 | 1 |
| GSM1061105 | 1 | postmenopausal | 6 | minor | 3 | 77 | ductal | 3 | 22 | 0 | 3 | 1.3 | 1 |
| GSM1061104 | 0 | postmenopausal | 6 | minor | 2 | 60 | ductal | equivocal | 9 | 0 | 0 | 0.1 | 1 |
| GSM1061103 | 0 | postmenopausal | 6 | average for age | 2 | 75 | ductal | 3 | 25 | 0 | 2 | 0.9 | 1 |
| GSM1061102 | 1 | NA | 6 | minor | 3 | 63 | ductal | 3 | 18 | 1 | 1 | 0.8 | 1 |
| GSM106110 | 1 | postmenopausal | 6 | perfect health | 2 | 66 | ductal | 1 | 15 | 0 | 0 | -0.6 | 1 |
| GSM1061100 | 0 | premenopausal | 6 | perfect health | 3 | 49 | ductal | 3 | 15 | 1 | 2 | 0.8 | 0 |
| GSM1061099 | 1 | premenopausal | 9 | perfect health | 2 | 47 | ductal | 3 | 20 | 0 | 0 | 0.4 | 1 |
| GSM1061098 | 1 | postmenopausal | 9 | perfect health | 2 | 55 | ductal | 3 | 17 | 0 | 0 | 2 | 1 |
| GSM1061097 | 0 | premenopausal | 9 | perfect health | 2 | 44 | ductal | 3 | 26 | 0 | 0 | 0.7 | 1 |
| GSM1061096 | 1 | postmenopausal | 9 | perfect health | 2 | 64 | ductal | 1 | 13 | 0 | 0 | -1 | 1 |
| GSM1061095 | 0 | postmenopausal | 9 | perfect health | 2 | 64 | ductal | 3 | 32 | 0 | 1 | 0.4 | 1 |
| GSM1061094 | 1 | premenopausal | 9 | perfect health | 1 | 49 | ductal | 1 | 21 | 0 | 0 | -0.6 | 1 |
| GSM1061093 | 1 | premenopausal | 9 | perfect health | 2 | 44 | ductal | 1 | 15 | 0 | 0 | -0.6 | 1 |
| GSM1061092 | 1 | premenopausal | 9 | perfect health | 2 | 44 | ductal | 3 | 25 | 0 | 0 | 1.1 | 1 |
| GSM106109 | 1 | premenopausal | 9 | perfect health | 2 | 42 | lobular | 1 | 17 | 0 | 0 | -1.2 | 1 |
| GSM1061090 | 0 | premenopausal | 9 | perfect health | 3 | 31 | ductal | 3 | 23 | 0 | 0 | 2.8 | 0 |
| GSM1061089 | 1 | premenopausal | 9 | perfect health | 2 | 53 | ductal | equivocal | 19 | 0 | 0 | -0.1 | 1 |
| GSM1061088 | 0 | postmenopausal | 9 | average for age | 3 | 82 | lobular | 1 | 27 | 0 | 0 | -0.3 | 0 |
| GSM1061087 | 1 | postmenopausal | 9 | perfect health | 1 | 64 | ductal | 1 | 12 | 0 | 0 | -0.8 | 1 |
| GSM1061086 | 1 | postmenopausal | 9 | perfect health | 2 | 61 | ductal | 1 | 15 | 0 | 0 | -0.4 | 1 |
| GSM1061085 | 0 | postmenopausal | 9 | perfect health | 3 | 73 | lobular | 3 | 22 | 0 | 0 | 0.4 | 1 |
| GSM1061084 | 0 | postmenopausal | 9 | average for age | 3 | 82 | ductal | 3 | 22 | 1 | 0 | 0.4 | 0 |
| GSM1061083 | 1 | postmenopausal | 9 | perfect health | 2 | 65 | ductal | 1 | 11 | 0 | 1 | -2.2 | 1 |
| GSM1061082 | 0 | premenopausal | 9 | perfect health | 3 | 35 | ductal | 3 | 22 | 0 | 1 | 2.9 | 1 |
| GSM106108 | 1 | postmenopausal | 2 | perfect health | 2 | 61 | ductal | equivocal | 25 | 0 | 1 | -0.1 | 1 |
| GSM1061080 | 1 | premenopausal | 2 | minor | 1 | 48 | ductal | 1 | 10 | 0 | 0 | -2.5 | 1 |
| GSM1061079 | 1 | postmenopausal | 2 | minor | 2 | 58 | ductal | equivocal | 30 | 0 | 1 | 0.2 | 1 |
| GSM1061078 | 1 | premenopausal | 2 | minor | 2 | 47 | ductal | equivocal | 17 | 0 | 0 | -0.1 | 1 |
| GSM1061077 | 1 | postmenopausal | 1 | minor | 3 | 71 | ductal | equivocal | 42 | 0 | 0 | 0.1 | 1 |
| GSM1061076 | 0 | postmenopausal | 1 | average for age | 2 | 71 | ductal | equivocal | 12 | 0 | 0 | -0.1 | 0 |
| GSM1061075 | 1 | postmenopausal | 1 | average for age | 3 | 78 | ductal | 3 | 42 | 1 | 0 | 0.6 | 1 |
| GSM1061074 | 1 | premenopausal | 1 | minor | 2 | 49 | ductal | equivocal | 15 | 0 | 0 | -0.2 | 1 |
| GSM1061073 | 1 | postmenopausal | 1 | average for age | 3 | 55 | ductal | 3 | 12 | 0 | 0 | 1.3 | 1 |
| GSM1061072 | 1 | postmenopausal | 1 | average for age | 3 | 73 | ductal | 3 | 40 | 0 | 3 | 1.5 | 1 |
| GSM106107 | 1 | premenopausal | 1 | perfect health | 1 | 42 | ductal | 1 | 41 | 0 | 0 | -0.8 | 1 |
| GSM1061070 | 1 | postmenopausal | 1 | major problems | 1 | 81 | ductal | equivocal | 14 | 0 | 0 | -0.2 | 1 |
| GSM1061069 | 1 | premenopausal | 6 | minor | 3 | 42 | ductal | equivocal | 17 | 0 | 0 | 0.2 | 1 |
| GSM1061068 | 1 | postmenopausal | 6 | average for age | 1 | 78 | lobular | equivocal | 19 | 0 | 0 | -0.3 | 1 |
| GSM1061067 | 1 | premenopausal | 6 | perfect health | 3 | 53 | ductal | 3 | 21 | 0 | 1 | 0.4 | 1 |
| GSM1061066 | 0 | postmenopausal | 9 | perfect health | 2 | 50 | ductal | 1 | 15 | 1 | 0 | -0.3 | 1 |
| GSM1061065 | 0 | premenopausal | 9 | perfect health | 2 | 39 | ductal | 3 | 13 | 0 | 0 | 2.4 | 0 |
| GSM1061064 | 1 | postmenopausal | 9 | perfect health | 2 | 53 | lobular | equivocal | 28 | 0 | 3 | -0.2 | 1 |
| GSM1061063 | 1 | premenopausal | 9 | perfect health | 3 | 41 | ductal | 3 | 28 | 0 | 1 | 1.5 | 1 |
| GSM1061062 | 0 | premenopausal | 9 | perfect health | 3 | 46 | ductal | 3 | 32 | 0 | 0 | 3.1 | 0 |
| GSM106106 | 0 | postmenopausal | 3 | minor | 1 | 66 | ductal | 1 | 9 | 0 | 0 | -2 | 1 |
| GSM1061060 | 0 | postmenopausal | 3 | major problems | 3 | 69 | ductal | 3 | 21 | 0 | 0 | 3.1 | 0 |
| GSM1061059 | 1 | postmenopausal | 3 | major problems | 2 | 60 | ductal | 3 | 24 | 0 | 0 | 0.6 | 1 |
| GSM1061058 | 1 | postmenopausal | 3 | minor | 3 | 54 | lobular | 3 | 35 | 0 | 0 | 0.9 | 1 |
| GSM1061057 | 1 | postmenopausal | 3 | NA | 3 | 71 | ductal | 3 | 19 | 0 | 0 | 1.5 | 1 |
| GSM1061056 | 1 | postmenopausal | 3 | average for age | 1 | 76 | ductal | equivocal | 24 | 0 | 0 | -0.2 | 1 |
| GSM1061055 | 1 | postmenopausal | 3 | perfect health | 1 | 78 | ductal | equivocal | 18 | 0 | 0 | -0.3 | 1 |
| GSM1061054 | 1 | postmenopausal | 8 | perfect health | 3 | 73 | ductal | 1 | 44 | 0 | 3 | -0.6 | 1 |
| GSM1061053 | 0 | premenopausal | 2 | minor | 3 | 48 | ductal | 3 | 11 | 0 | 0 | 1.2 | 0 |
| GSM1061052 | 1 | postmenopausal | 2 | minor | 2 | 56 | ductal | equivocal | 16 | 1 | 2 | 0.3 | 1 |
| GSM106105 | 1 | postmenopausal | 2 | minor | 2 | 77 | ductal | 1 | 11 | 0 | 1 | -1 | 1 |
| GSM1061050 | 1 | premenopausal | 2 | minor | 2 | 51 | ductal | 1 | 28 | 0 | 1 | -1.5 | 1 |
| GSM1061049 | 1 | postmenopausal | 2 | minor | 1 | 67 | ductal | 1 | 18 | 0 | 0 | -2.3 | 1 |
| GSM1061048 | 1 | premenopausal | 2 | perfect health | 2 | 48 | ductal | equivocal | 10 | 0 | 0 | 0 | 1 |
| GSM1061047 | 1 | postmenopausal | 6 | perfect health | 3 | 67 | ductal | 1 | 18 | 0 | 1 | -0.4 | 1 |
| GSM1061046 | 0 | postmenopausal | 6 | perfect health | 2 | 66 | ductal | 3 | 50 | 0 | 0 | 0.7 | 1 |
| GSM1061045 | 1 | postmenopausal | 6 | minor | 1 | 72 | ductal | 1 | 11 | 0 | 3 | -1.8 | 1 |
| GSM1061044 | 1 | NA | 6 | perfect health | 2 | 53 | ductal | 1 | 12 | 0 | 0 | -1.3 | 1 |
| GSM1061043 | 0 | postmenopausal | 6 | minor | 3 | 54 | ductal | 3 | 45 | 1 | 0 | 1.5 | 0 |
| GSM1061042 | 0 | postmenopausal | 6 | perfect health | 2 | 61 | ductal | 3 | 10 | 0 | 0 | 0.6 | 1 |
| GSM106104 | 1 | postmenopausal | 1 | major problems | 2 | 81 | lobular | equivocal | 15 | 0 | 0 | 0.1 | 1 |
| GSM1061040 | 1 | premenopausal | 1 | minor | 2 | 47 | ductal | equivocal | 13 | 0 | 0 | 0 | 1 |
| GSM1061039 | 0 | postmenopausal | 1 | NA | 3 | 90 | ductal | 3 | 18 | NA | 0 | 0.4 | 0 |
| GSM1061038 | 1 | postmenopausal | 1 | minor | 2 | 61 | lobular | 1 | 11 | 0 | 0 | -0.8 | 1 |
| GSM1061037 | 1 | postmenopausal | 1 | average for age | 1 | 76 | lobular | 1 | 16 | 0 | 0 | -2.2 | 1 |
| GSM1061036 | 0 | NA | 1 | perfect health | 3 | 43 | ductal | 3 | 19 | 0 | 0 | 2.5 | 0 |
| GSM1061035 | 1 | postmenopausal | 1 | average for age | 2 | 65 | ductal | 1 | 30 | 0 | 0 | -0.6 | 1 |
| GSM1061034 | 0 | postmenopausal | 4 | average for age | 2 | 59 | ductal | 3 | 10 | 1 | 0 | 0.5 | 0 |
| GSM1061033 | 1 | postmenopausal | 4 | major problems | 2 | 60 | ductal | 3 | 22 | 0 | 0 | 2.2 | 1 |
| GSM1061032 | 1 | postmenopausal | 6 | perfect health | 2 | 68 | ductal | 3 | 17 | 0 | 0 | 0.7 | 1 |