Introduction
Methods
Study population
Laboratory methods
Variant classification
Statistical analysis
Breast cancer risk estimation
Results
Demographics
Demographic |
N
| Total | % |
---|---|---|---|
Ethnicity | |||
Caucasian | 468 | 708 | 66.1 |
Ashkenazi Jewish | 70 | 708 | 9.9 |
African American | 58 | 708 | 8.2 |
Asian | 23 | 708 | 3.2 |
Hispanic | 16 | 708 | 2.3 |
Middle Eastern | 5 | 708 | 0.7 |
Native American | 1 | 708 | 0.1 |
Mixed ethnicity | 20 | 708 | 2.8 |
Other | 3 | 708 | 0.4 |
Unknown | 44 | 708 | 6.2 |
Panel ordered (total number of genes on panel) | |||
BRCAplus (5–6) | 115 | 708 | 16.2 |
GYNplus (9–13) | 7 | 708 | 1.0 |
BRCAplus-expanded | 17 | 708 | 2.4 |
BreastNext (14–18) | 297 | 708 | 41.9 |
OvaNext (19–24) | 66 | 708 | 9.3 |
PancNext (range) | 5 | 708 | 0.7 |
CancerNext (22–32) | 148 | 708 | 20.9 |
CancerNext-expanded (43–49) | 53 | 708 | 7.5 |
Age at testing | |||
20–29 | 2 | 708 | 0.3 |
30–39 | 18 | 708 | 2.5 |
40–49 | 43 | 708 | 6.1 |
50–59 | 138 | 708 | 19.5 |
60–69 | 234 | 708 | 33.1 |
70–79 | 189 | 708 | 26.7 |
80–89 | 75 | 708 | 10.6 |
90 and older | 9 | 708 | 1.3 |
Age at diagnosisa
| |||
20–29 | 10 | 687 | 1.5 |
30–39 | 28 | 687 | 4.1 |
40–49 | 70 | 687 | 10.2 |
50–59 | 160 | 687 | 23.3 |
60–69 | 210 | 687 | 30.6 |
70–79 | 158 | 687 | 23.0 |
80–89 | 47 | 687 | 6.8 |
90 and older | 4 | 687 | 0.6 |
Testing history | |||
Prior BRCA1/2 testing | 223 | 708 | 31.5 |
Clinical Historya
| |||
Family history male breast cancer | 41 | 643 | 6.4 |
Multiple primary breast cancers | 28 | 706 | 4.0 |
Additional non-breast primary cancers | 166 | 708 | 23.4 |
Test results
Positive gene(s) | Pathogenic variant(s) | First breast cancer age | Bilateral/multiple breast cancers | Other cancer(s) | Family history of MBCa
| Ethnicity | Notes |
---|---|---|---|---|---|---|---|
ATM
| p.K2756* | 70–79 | No | Liver/melanoma/prostate | NP | Caucasian | |
ATM
| p.R2832C | 60–69 | No | No | Caucasian | ||
ATM
| c.901+1G>A | 70–79 | No | No | Hispanic | ||
ATM/ATM
| c.5763-1050A>G/c.8418+5_8418+8delGTGA | 50–59 | No | No | Caucasian | AT clinical dx | |
ATM/BRCA2
| p.W2638*/c.5616_5620delAGTAA | 70–79 | No | Prostate | No | African American | |
ATM/BRCA2
| p.Q2651*/p.Q548* | 80–89 | No | Skin | No | Caucasian | |
BARD1
| p.Q564* | 70–79 | No | NP | Caucasian | ||
BARD1/PALB2
| c.1935_1954dup20/c.109-2A>G | 50–59 | No | Yes | Unknown | ||
BRCA1
| EX11_13del | 50–59 | No | No | Caucasian | ||
BRCA1
| p.C61G | 60–69 | No | No | Caucasian | ||
BRCA1
| EX11_13del | 60–69 | No | No | Caucasian | ||
BRCA1
| c.5266dupC | 60–69 | No | No | Caucasian | ||
BRCA1
| c.3481_3491del11 | 60–69 | No | Liver | No | Caucasian | |
BRCA1/CHEK2
| c.5177_5180delGAAA/c.1100delC | 40–49 | No | No | African American | ||
BRCA2
| 5′UTR_EX1del | 50–59 | No | Bladder | NP | Caucasian | |
BRCA2
| c.5576_5579delTTAA | 60–69 | No | NP | Caucasian | ||
BRCA2
| c.9253dupA | 60–69 | No | NP | African American | ||
BRCA2
| p.R2520* | 60–69 | Yes | NP | Middle Eastern | ||
BRCA2
| c.1813dupA | 70–79 | No | Prostate | NP | Caucasian | |
BRCA2
| 5′UTR_EX1del | 60–69 | No | Gastroesophageal | No | Caucasian | |
BRCA2
| c.518delG | 60–69 | No | Leukemia | No | African American | |
BRCA2
| c.1296_1297delGA | 60–69 | No | No | Caucasian | ||
BRCA2
| p.D2723H | 30–39 | No | No | Caucasian | ||
BRCA2
| c.7865dupA | 40–49 | No | Bladder | No | Asian | |
BRCA2
| c.4456_4459delGTTA | 40–49 | Yes | No | African American | ||
BRCA2
| c.3257_3258delTA | 40–49 | Yes | No | African American | ||
BRCA2
| c.5164_5165delAG | 50–59 | No | No | African American | ||
BRCA2
| c.5722_5723delCT | 50–59 | No | Tonsil/NOS | No | Caucasian | |
BRCA2
| c.5946delT | 50–59 | No | Ureter | No | Ashkenazi Jewish | |
BRCA2
| 5′UTR_EX15del | 50–59 | No | No | Ashkenazi Jewish | ||
BRCA2
| c.8297delC | 50–59 | No | Lymphoma | No | Caucasian | |
BRCA2
| c.8297delC | 50–59 | No | Skin | No | Caucasian | |
BRCA2
| c.8331+1G>A | 50–59 | No | Pancreas/melanoma | No | Caucasian | |
BRCA2
| p.E1953* | 50–59 | No | No | Caucasian | ||
BRCA2
| c.6938-1G>A | 50–59 | No | Tonsil | No | Mixed ethnicity | |
BRCA2
| c.5799_5802delCCAA | 60–69 | No | No | Hispanic | ||
BRCA2
| c.5130_5133delTGTA | 60–69 | No | No | Caucasian | ||
BRCA2
| 5′UTR_EX1del | 60–69 | No | No | Caucasian | ||
BRCA2
| c.6676_6677delGA | 60–69 | No | No | Caucasian | ||
BRCA2
| c.5722_5723delCT | 60–69 | No | Prostate | No | Caucasian | |
BRCA2
| c.7977-1G>C | 60–69 | No | Yes | Caucasian | ||
BRCA2
| c.6591_6592delTG | 60–69 | No | No | Caucasian | ||
BRCA2
| c.4940_4941delCA | 60–69 | No | No | Mixed ethnicity | ||
BRCA2
| p.E1308* | 60–69 | No | No | Unknown | ||
BRCA2
| c.1813dupA | 60–69 | No | No | Caucasian | ||
BRCA2
| c.5350_5351delAA | 60–69 | Yes | No | Caucasian | ||
BRCA2
| p.V159M | 60–69 | No | No | Hispanic | ||
BRCA2
| c.9117G>A | 60–69 | No | No | Caucasian | ||
BRCA2
| p.R2336P | 60–69 | No | No | Other | ||
BRCA2
| c.8374_8384del11insAGG | 60–69 | No | Prostate | No | Caucasian | |
BRCA2
| p.R2520* | 70–79 | No | Prostate | Yes | Caucasian | |
BRCA2
| p.E3111* | 70–79 | Yes | Yes | African American | ||
BRCA2
| c.4876_4877delAA | 70–79 | Yes | Colon/lymphoma | No | Caucasian | |
BRCA2
| c.778_779delGA | 70–79 | No | No | Caucasian | ||
BRCA2
| p.R2659K | 70–79 | No | Prostate | No | Caucasian | |
BRCA2
| c.3975_3978dupTGCT | 70–79 | No | No | Caucasian | ||
BRCA2
| p.Q2859* | 70–79 | No | No | Caucasian | ||
BRCA2
| p.E49* | 70–79 | No | No | Mixed ethnicity | ||
BRCA2
| c.9435_9436delGT | 70–79 | No | Melanoma/skin | No | Caucasian | |
BRCA2
| c.6068_6072delACCAG | 70–79 | No | Bladder | No | Caucasian | |
BRCA2
| c.1929delG | 70–79 | No | Melanoma/skin | No | Caucasian | |
BRCA2
| c.3975_3978dupTGCT | 70–79 | No | Colon/lung | Yes | Unknown | |
BRCA2
| p.Q3026* | 90–99 | No | Yes | Mixed ethnicity | ||
BRCA2
| p.R2520* | 90–99 | No | No | Caucasian | ||
BRCA2
| c.5946delT | NOS | No | No | Unknown | ||
BRCA2
| c.4876_4877delAA | NOS | Yes | No | Hispanic | ||
BRCA2/BRIP1
| c.2808_2811delACAA/p.R798* | 70–79 | No | Yes | Caucasian | ||
CHEK2
| c.591delA | 60–69 | No | NP | Caucasian | ||
CHEK2
| p.R117G | 40–49 | No | No | Caucasian | ||
CHEK2
| c.1100delC | 40–49 | No | No | Caucasian | ||
CHEK2
| c.1100delC | 40–49 | No | No | Caucasian | ||
CHEK2
| c.1100delC | 40–49 | No | No | Caucasian | ||
CHEK2
| p.T476M | 50–59 | No | Melanoma | No | Unknown | |
CHEK2
| c.1100delC | 50–59 | No | Kidney | No | Caucasian | |
CHEK2
| p.I157T | 50–59 | No | No | Caucasian | ||
CHEK2
| p.T476M | 50–59 | No | Colon | No | Caucasian | |
CHEK2
| p.I157T | 50–59 | No | No | Caucasian | ||
CHEK2
| c.1100delC | 50–59 | No | No | Caucasian | ||
CHEK2
| p.I157T | 50–59 | No | No | Ashkenazi Jewish | ||
CHEK2
| c.1100delC | 60–69 | No | Leukemia | No | Caucasian | |
CHEK2
| p.S428F | 60–69 | No | No | Ashkenazi Jewish | ||
CHEK2
| c.1100delC | 60–69 | No | No | Caucasian | ||
CHEK2
| p.Q29* | 70–79 | No | No | Caucasian | ||
CHEK2
| p.S428F | 70–79 | No | Yes | Ashkenazi Jewish | ||
CHEK2
| p.I157T | 70–79 | No | No | Caucasian | ||
CHEK2
| p.I157T | 70–79 | No | No | Caucasian | ||
CHEK2
| c.1100delC | <59 | No | Yes | Caucasian | ||
CHEK2/PALB2
| p.I157T/c.172_175delTTGT | 70–79 | No | No | Caucasian | ||
MRE11A
| c.1867+2T>C | 70–79 | No | No | Caucasian | ||
NBN
| c.657_661delACAAA | 70–79 | No | No | Caucasian | ||
NF1
| p.R1276* | 50–59 | No | NP | African American | ||
NF1
| p.Q1070* | 30–39 | No | No | African American | NF1 clinical dx | |
NF1
| c.1721+3A>G | 40–49 | No | Leukemia/pheochromocytoma/lymphoma | No | Mixed ethnicity | Son noted to have NF1 clinical dx |
PALB2
| c.661_662delinsTA | 50–59 | No | Thyroid | No | Caucasian | |
PALB2
| p.Y1183* | 50–59 | No | No | Ashkenazi Jewish | ||
PALB2
| c.93dupA | 60–69 | No | No | Caucasian | ||
RAD51D
| c.270_271dupTA | 80–89 | No | No | Asian |
Gene | No prior BRCA1/2 testing | Prior BRCA1/2 testing | All MBC | ||||||
---|---|---|---|---|---|---|---|---|---|
Total pathogenic/likely pathogenic variants | Total testeda
| % | Total pathogenic/likely pathogenic variants | Total testeda
| % | Total pathogenic/likely pathogenic variants | Total testeda
| % | |
BRCA2
| 53 | 480 | 11.0 | 2 | 197 | 1.0 | 55 | 677 | 8.1 |
CHEK2 (all) | 16 | 386 | 4.1 | 6 | 195 | 3.1 | 22 | 581 | 3.8 |
CHEK2 (excluding I157T) | 11 | 386 | 2.8 | 5 | 195 | 2.6 | 16 | 581 | 2.8 |
CHEK2 (I157T only) | 5 | 386 | 1.3 | 1 | 195 | 0.5 | 6 | 581 | 1.0 |
ATM
b
| 6 | 390 | 1.5 | 0 | 196 | 0.0 | 6 | 586 | 1.0 |
BRCA1
| 6 | 480 | 1.3 | 0 | 197 | 0.0 | 6 | 677 | 0.9 |
NF1
| 2 | 354 | 0.6 | 1 | 158 | 0.6 | 3 | 512 | 0.6 |
PALB2
| 2 | 417 | 0.5 | 3 | 204 | 1.5 | 5 | 621 | 0.8 |
RAD51D
| 1 | 354 | 0.3 | 0 | 158 | 0.0 | 1 | 512 | 0.2 |
BRIP1
| 1 | 370 | 0.3 | 0 | 194 | 0.0 | 1 | 564 | 0.2 |
MRE11A
| 1 | 370 | 0.3 | 0 | 194 | 0.0 | 1 | 564 | 0.2 |
NBN
| 1 | 370 | 0.3 | 0 | 194 | 0.0 | 1 | 564 | 0.2 |
BARD1
| 0 | 370 | 0.0 | 2 | 194 | 1.0 | 2 | 564 | 0.4 |
Diagnostic yield
Result category | No prior BRCA testing (n = 354) | Prior BRCA testing (n = 158) | ||
---|---|---|---|---|
N
| % |
N
| % | |
Pathogenic/likely pathogenic variant | 64 | 18.1 | 12 | 7.6 |
Pathogenic/likely pathogenic variant(s) in a single gene | 60a
| 16.9 | 11 | 7.0 |
BRCA1/2
| 39 | 11.0 | 2 | 1.3 |
Non-BRCA1/2
| 21 | 5.9 | 9 | 5.7 |
Pathogenic/likely pathogenic variant(s) in multiple genes | 4 | 1.1 | 1 | 0.6 |
Combination of BRCA1/2 and non-BRCA1/2 genes | 3 | 0.8 | 0 | 0.0 |
Multiple non-BRCA1/2 genes | 1 | 0.3 | 1 | 0.6 |
Pathogenic/likely pathogenic variant + VUS | 16 | 4.5 | 5 | 3.2 |
VUS only | 59 | 16.7 | 34 | 21.5 |
Negative | 231 | 65.3 | 112 | 70.9 |
Clinical history comparisons
Gene-specific risks of MBC
Gene | Ambry cases | ExAC controls | Cancer risk | |||||
---|---|---|---|---|---|---|---|---|
Mutated alleles | Cases | Mutated alleles | Cases | OR | 95% CI lower | 95% CI upper |
p value | |
ATM
| 2 | 421 | 90 | 26,644 | 1.4 | 0.3 | 5.1 | 0.66 |
BRCA1
| 2 | 394 | 74 | 26,911 | 1.8 | 0.3 | 6.8 | 0.30 |
BRCA2
| 21 | 394 | 105 | 26,791 | 13.9 | 8.5 | 22.5 | 1.92 × 10−16
|
CHEK2 All | 17 | 421 | 424 | 25,215 | 2.4 | 1.4 | 3.9 | 1.82 × 10−3
|
CHEK2_c.1100delC | 8 | 421 | 127 | 25,215 | 3.8 | 1.7 | 7.8 | 1.82 × 10−3
|
CHEK2 W/O I157T/S428F | 10 | 421 | 163 | 25,215 | 3.7 | 1.9 | 7.0 | 6.24 × 10−4
|
CHEK2 W/O I157T | 12 | 421 | 191 | 25,215 | 3.8 | 2.1 | 6.8 | 1.51 × 10−4
|
CHEK2 I157T | 5 | 421 | 233 | 25,215 | 1.3 | 0.5 | 3.0 | 0.60 |
PALB2
| 3 | 421 | 29 | 26,869 | 6.6 | 1.7 | 21.1 | 0.013 |