CGN DNA Bank Summary
February 16, 2010
Summary
The Cancer Genetics Network (CGN) DNA Bank was initiated in 2007 to collect DNA
samples from CGN registrants with multiple primary and early-onset cancer diagnoses.
This population was selected because subjects with a history of multiple primaries and
early-onset cancers are more likely to have genetic susceptibility to cancer. In 2009, the
DNA Bank was expanded to include registrants with rare cancer diagnoses.
Procedures
Subjects from the CGN were consented for the CGN Bank following confirmation of
their eligibility by one of 13 CGN clinical centers. Blood or saliva samples were then
collected either in clinic or remotely. These samples were shipped fresh to the Partners
Center for Personalized Genetic Medicine (PCPGM) where DNA was extracted, frozen,
and stored.
DNA Summary
DNA has been extracted and stored for 748 subjects. For 715 subjects, DNA is stored in 2
or more aliquots; 33 subjects have only 1 aliquot. The mean quantity of DNA stored per
patient is 333 ug (standard deviation: 309 ug). Total quantities per patient range from 1.1
ug to 4656 ug (median: 261 ug). DNA purity is calculated as the ratio of light absorption
at 260 nm and 280 nm. This provides an estimate of protein contamination of the DNA.
Standard purity is 1.8. The CGN DNA bank samples have a mean purity of 1.8 (standard
deviation: 0.2). Purity ranges from 0.6 to 5.8 (10th percentile: 1.7).
Table 1. Summary of Enrollment by Eligibility Category (Data available for 639
subjects)
Category
N
1. Multiple Early Onset Cancers & Family History of Same
7
2. Multiple Early Onset Cancer & Family History of Early Onset
20
3. Early Onset Cancer & Family History of Multiple Early Onset Cancers
25
4. Early Onset Cancer & Family History of Same
79
5. Primary Cancer & Family History of Same Type
83
6. Multiple Early Onset Cancers & No Family History
49
7. Early Onset Cancer & No Family History
230
8. Rare Cancer*
156
Other
5
* Note that subjects with rare cancers may also be listed in one of categories 1 – 7.
Table 2. Summary of Rare Cancers
Type
Bladder
Bone
Brain
Dermatofibrosarcoma
Eccrine tumor of breast
Esophagus
Head/Neck
Kidney
Leiomyosarcoma
Malt lymphoma
Melanoma
Myxoid liposarcoma
Pancreas
Papillary adrenal carcinoma
Placenta
Salivary gland
Scrotum
Sebaceous carcinoma
Soft tissue
Stomach
Thymus
Thyroid
Vulva
TOTAL
** Data missing for 8 subjects
N
1
1
4
1
1
4
1
21
2
1
26
1
48
1
1
1
1
1
2
1
1
26
1
148**
Table 3. Cancer Types by Eligibility Category
The following table gives frequencies of cancer types for each eligibility category (see
Table 1). Note that only cancer diagnoses in the enrollee are reported for categories 1-4
and 6-7. Participants are counted for as many cancer types as s/he has. In category 5
(Primary Cancer & Family History of Same Type), frequencies of the cancer common
between enrollee and family members are given.
Cancer Type
Anus
Biliary Tract
Bladder
Bone
Brain
Breast
Cervix
Colon
Endocrine
Female Genital
Gastrointestinal
Head
Hematologic
Intestine
Kidney
Lip
Lung
Lymph
Melanoma
Mouth
Ovary
Pancreas
Prostate
Rectum
Respiratory Tract
Skin (non-melanoma)
Soft Tissue
Testes
Uterus
Unknown
1
Eligibility Categories
3
4
5
1
2
6
7
2
1
5
1
1
1
12
1
6
2
1
25
1
1
1
66
6
7
2
1
8
1
2
1
1
2
46
4
4
6
2
173
12
21
10
1
1
1
4
1
1
1
3
1
3
8
5
1
2
2
1
3
1
1
1
16
4
30
1
6
19
2
3
2
3
1
7
8
6
1
3
1
1
1
8
1
12
2
1
1
1
4
1
3
6
9
2
2
2
2
1
26
1
18
2
4
10
19
1
2
5
1
Total
1
2
3
2
5
335
25
41
21
2
1
1
6
1
21
1
22
15
88
3
44
2
10
10
1
51
1
4
18
4