Appendix E - The Cancer Genome Atlas Forms - Lung.pdf

Draft V2.5 August 29, 2008 1

The Cancer Genome Atlas (TCGA) Clinical Data Reporting Form - Lung

Barcode

Internal Use Only

Tissue Source Site (TSS) Name: ________________________

TSS Identifier #:

Tier 1 Clinical Data Definition: All of these elements (1-22) are required to “qualify” the tumor specimen for TCGA project.

1. Completed By:

Date: / /

M M D D Y Y

2. Completed By:

Date:

M M D D Y Y

Tier # Data Element Label Entry Alternatives caBIG Definition

1: 01 TSS Unique Patient #

1: 02 Organ of Origin – Lung Brain

Lung

Ovary

Whole organ level. Text term for originating or primary anatomic site of the disease/condition under investigation or review. (2735776)

1: 03 Histological Type: Lung

Confirm squamous carcinoma

Yes

No

The description of the microscopic pattern indicating the degree of similarity between the tumor and the tissue of origin.

1:04 Gender

Male

Female

Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis on their social roles. [

Explanatory Comment 1: Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc. (2200604)

1: 05 Date of Birth

M M D D Y Y

Date on which the patient/participant was born.

(2201154)

1: 06 Reserved for Future Use

N/A

1: 07 Tobacco smoking history indicator

Current

Former

Never

Text indicator to represent a person’s tobacco smoking, the act of puffing and/or inhaling smoke from a lit tobacco cigarette, cigar, or pipe. (2436233)

1: 08 Date of initial pathologic diagnosis

The date this disease was first diagnosed. (58204)

1: 09 Neo-adjuvant (pre-operative) therapy

Therapy includes any of the following: Radiation/

Chemo/ Immuno/ Hormonal Therapy. The yes/no indicator to ask whether any treatment was given the patient prior to surgery.

1: 10 Date of Surgical Resection

The date of a surgical procedure.

Tier 1 Clinical Data (Page 1 of 3)

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TCGA Clinical Data Reporting Form - Lung

TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

1: 11A Tumor stage (pathological)

LUNG AJCC System

(Definitions are 6 th edition nomenclature)

Primary Tumor (T)

TX

TO

Tis

T1

T2

T3

Regional Nodes (N)

NX

NO

N1

N2

N3

Distant Metastasis (M)

MX

MO

M1

1: 11B Stage groupings (Definitions are 6 th edition nomenclature)

Occult (O)

I A

IB

IIA

II B

III A

III B

IV

1:12 Tumor Grade

For squamous of the Lung: N/A as a Tier 1 element (see q. 2.12)

NA

1: 13 Complete Excision (RO) Yes (RO)

No (R1)

Unknown

RO: Surgical margins free of tumor grossly and microscopically. No evidence of residual disease following surgery.

R1: Residual disease present (local, regional, or distant)

New CDE to be created

1: 14 Adjuvant (Post-operative)

Irradiation therapy

Yes

No Yes/no indicator to ask if therapeutic application if radiation was initiated to treat disease following surgery to remove tumor and associated malignant tissue.

Tier 1 Clinical Data (Page 2 of 3)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

1: 15 Adjuvant (Post-operative)

Chemotherapy

Yes

No Did the patient receive adjuvant chemotherapy?

1: 16 Adjuvant (Post-operative)

Immunotherapy

Yes

No Yes/no indicator that asks whether the patient has previous immunotherapy as preventive treatment for an earlier stage for this cancer.

1: 17 Adjuvant (Post-operative)

Hormonal therapy

Yes

No Yes/no/unknown indicator whether adjuvant hormone therapy was administered following surgery

1: 18

Adjuvant (Post-operative)

“Targeted” Molecular

Therapy

1: 19 Date of first Recurrence after therapy

N/A

The date when the return or spread of cancer was first diagnosed.

1: 20 Date of last contact

(clinical evaluation)

The date of the last successful contact with the patient, family member, or caregiver to establish responses for 1:21 and 1:22 below

1: 21 Vital Status Living

Deceased

Test summary level description of patient / participant survival status

1: 22 Date of Death NA

The actual date of a patients/participants death

Comments:

Principal Investigator Signature Print Name M M D D Y Y

Tier 1 Clinical Data (Page 3 of 3)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

Tissue Source Site (TSS) Name: ________________________

TSS Identifier #:

TSS Unique Patient # __________________________

Tier 2 Clinical Data Definition: Desirable, but not manditory clinical information for clinical correlation analyses.

1. Completed By:

Date: / /

M M D D Y Y

2. Completed By:

Date:

2: 02 Anatomic Organ Sub-

Division

a. Brain

b. Lung

c. Ovary

Brain N/A

Lung R Upper Middle Lower

L Upper Lower

Ovary R

L

Anatomic organ: Text term for originating of primary anatomic site of the disease/condition under investigation or review. (2735776)

For tumors in paired organs, designates the side on which was obtained (2007875)

2: 07 Tobacco current use No: # years quit YRS

Yes: Pack Yrs

Not known

Pack years: The number of packs (of cigarettes) smoked per day times the number of years smoked (2546448)

No. years quit: Total time period during when an individual didn’t smoke, expressed in number of years. (2181903)

Pack years: (256448)

2: 08 Method of initial pathologic diagnosis

Cytology (e.g. Peritoneal or pleural fluid)

Fine needle aspiration biopsy

Incision biopsy

Excisional biopsy

Tumor resection

Other method, specify:

Unknown

Method: Name of the procedure used to secure tissue for the original pathologic diagnosis.

(2757941)

Other method: Test to describe a method used to secure tissue for an original pathologic diagnosis that is different from other methods.

(2757948)

2: 09A Neo-adjuvant

(pre-operative)

Irradiation therapy

No

Yes Type:

External beam

Impants

Radioisotopes

Combinaton

Other

Specify Source:___________________

Start Date: / /

End Date: / /

Dosage: centi-Gray / Rads mille-curie

# of fractions:

Name of the neo-adjuvant radiation therapy type administered preoperatively to an individual (2757957)

Other type: Name of neo-adjuvant radiation therapy type administered preoperatively that is different from other identified types

(2757964)

Start date: Date neo-adjuvant preoperative radiation therapy began. (2759142)

Stop date: Date neo-adjuvant preoperative radiation therapy ended. (2759144)

Dosage: Text description of the total dose of radiation therapy administered to an individual expressed as a dosage amount and unit of measure (UOM). (2721441)

Fractions: The total number of radiation therapy sessions (fractions) which the patient has completed to receive the required radiation dose to primary treatment fields. (61465)

Tier 2 Clinical Data (Page 1 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 09B Neo-adjuvant

(pre-operative)

Chemotherapy

Root of administration:

Oral

Intravenous (IV)

Intra-peritoneal (IP)

IV and IP

Other: Specify

End Date: / /

# of cycles give:

Drugs used Total dose given

Start Date: The date on which prior neo-adjuvant chemotherapy treatment started.

(62690)

Stop Date: The total number of cycles (courses) administered to the patient of a protocol specified drug or therapy agent. (62590)

Drug Used: Name of a neo-adjuvant agent administered to an individual. (2758212)

Total Dosage given: Agent total cumulative dose (1515)

2: 09C Neo-adjuvant

(pre-operative)

Hormone therapy

Start Date: the start date of neo-adjuvant hormone therapy. (2199659)

Stop Date: The date neo-adjuvant hormonal therapy ended. (2199665)

Drugs Used: Name of the neo-adjuvant hormonal prior therapy agent administered to an individual. (2758641)

# of cycles: The total number of cycles (courses) administered to the patient f a protocol specified drug of therapy agent. (1515)

Tier 2 Clinical Data (Page 2 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

Tier # Data Element Entry Alternatives caBIG Definition

2: 09D Neo-adjuvant

(pre-operative)

Immunotherapy

No

Yes

Start Date: Date that neo-adjuvant immunotherapy began. (2758923)

Stop Date: Date that neo-adjuvant immunotherapy ended. (2759147)

Drug Used: Name of a neo-adjuvant immunotherapy agent administered to an individual. (2759151)

Total Dosage given: Agent total cumulative dose (1515)

2: 11A Additional information beyond AJCC manual 6 th edition is included here in preparation for edition 7…:

(T): Size

Nodules in Ipsilateral (non-primary) lung lobe:

(T) Size Recorded

T): size in cm

(T )size not recorded

Unknown

2: 11C Metastasis:

Plural effusion with malignant cells

Distant Metastasis

2: 11D Vascular Invasion Negative for venous invasion

Positive for venous invasion

Unknown for venous invasion

An indicator to ask if large vessel or venous invasion was detected by surgery or presence in tumor specimen. (64358 information to be derived from pathology reports (CDE # 64358)

2: 11E Lymphatic Invasion Negative for lymphatic invasion

Positive for lymphatic invasion

Unknown for lymphatic invasion

An indicator to ask if malignant cells are present on small or thin-walled vessels suggesting lymphatic involvement. (64171)

2: 12 Tumor Grade GX: Grade cannot be assessed

G1: Well differentiated

G2: Moderately differentiated

G3: Poorly differentiated

G4: Undifferentiated

Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.

Tier 2 Clinical Data (Page 3 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 13 Tumor Margins N/A Some tumors may have additional specifics in the definitions of margin involved with tumor

2: 14 Neo-adjuvant

(pre-operative)

Irradiation therapy

No

Yes Type:

External beam

Impants

Radioisotopes

End Date: / /

Name of the neo-adjuvant radiation therapy type administered preoperatively to an individual (2757957)

Other type: Name of neo-adjuvant radiation therapy type administered preoperatively that is different from other identified types

(2757964)

Start date: Date neo-adjuvant preoperative radiation therapy began. (2759142)

Stop date: Date neo-adjuvant preoperative radiation therapy ended. (2759144)

Dosage: Text description of the total dose of radiation therapy administered to an individual expressed as a dosage amount and unit of measure (UOM). (2721441)

Fractions: The total number of radiation therapy sessions (fractions) which the patient has completed to receive the required radiation dose to primary treatment fields. (61465)

2: 15 Adjuvant (Post-operative)

Chemotherapy

Intravenous (IV)

Intra-peritoneal (IP)

IV and IP

Start Date: the start date for previous chemotherapy administered as preventive treatment for an earlier stage of this cancer.

(2285)

Stop Date: the end date for previous chemotherapy administered as preventive treatment for an earlier stage of this cancer.

(2287)

# of Cycles: The total number of cycles

(courses) administered to the patient of a protocol specified drug or therapy agent.

(62590)

Drug Used: the name of the agent or regimen of adjuvant Cytotoxic chemotherapy that was administered. (2464267)

Total Dose given: Agent total cumulative dose

(1515)

Tier 2 Clinical Data (Page 4 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 16 Adjuvant (Post-operative)

Immunotherapy

No

Yes

Start Date: The start date for previous immunotherapy administered as preventive treatment for an earlier stage of this cancer.

(2293)

Stop Date: The end date for previous immunotherapy administered as preventive treatment for an earlier stage of this cancer.

(2295)

Drug Used: Name of a adjuvant immunotherapy agent administered to an individual.[Manually-curated] (2759176)

# of Cycles: The total number of cycles

(courses) administered to the patient of a protocol specified drug or therapy agent.

(62590)

Total Dose given: Agent total cumulative dose

2: 17 Adjuvant (Post-Operative)

Hormone therapy

No

Yes

2: 18 Adjuvant (Post-operative)

Targeted Molecular Therapy

No

Yes

Specify:

Tier 2 Clinical Data (Page 5 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 21 Vital Status

A. Living

B. Dead

Living

Tumor Free

With Tumor

Unknown Tumor Status

Dead

Tumor Free

With Tumor

Unknown Tumor Status

The state or condition of an individual’s neoplasm at a particular point in time.

(2759550)

The state or condition of an individual’s neoplasm at a particular point in time.

(2759550)

2: 00A Race

Ethnicity

American Indian or Alaska Native (A person having origins in any of the original peoples of North and South America (including

Central America), and who maintains tribal affiliation or community attachment)

Asian (A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent including, for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam)

White (A person having origins in any of the original peoples of Europe, the Middle East, or

North Africa)

Black or African American (A person having origins in any of the black racial groups of

Africa. Terms such as "Haitian" or "Negro" can be used in addition to "Black or African American.")

Native Hawaiian or other Pacific Islander ( A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific

Islands)

Not Reported (Not provided or available)

Unknown (Could not be determined or unsure)

Not Hispanic or Latino (A person not meeting the definition for Hispanic or Latino)

Hispanic or Latino (A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race)

Not reported (Not provided or available)

Unknown (Could not be determined or unsure)

Race (2192199)

Ethnicity (2192217)

Tier 2 Clinical Data (Page 6 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 00B Patient Performance Status

Scale

Not Recorded

a. Karnofsky Score

100 asymptomatic

80-90 symptomatic by fully ambulatory

60-70 symptomatic but in bed less then

50% of day

40-50 symptomatic, in bed more than 50% of the day, but not bed ridden

20-30 bed ridden

b. Eastern Cancer Oncology Group

(ECOG)

0 asymptomatic

1 symptomatic by fully ambulatory

2 symptomatic but in bed less then

50% of day

3 symptomatic, in bed more than 50% of the day, but not bed ridden

4 bed ridden

Performance status scale, representing the functional capabilities of a person. (2003853)

2: 00C Second Surgery for tumor recurrence or progression

None

Local site procedure

No / /

Yes M M D D Y Y

Lymph Node procedure

No / /

Yes M M D D Y Y

Metastasis procedure

No / /

Yes M M D D Y Y

Indicator: The yes/no/unknown indicator that asks whether the recurrence was treated by surgery. (2199761)

Procedure: Name of the second surgical procedure performed for recurrent or progressive disease. (2759612)

Date: Date of the second surgical procedure performed for recurrent or progressive disease.

(2759616)

2: 00D Additional treatment of tumor recurrence/progression

Irradiation therapy

No

Yes Type:

External beam

Impants

Radioisotopes

End Date: / /

Indicator: the yes/no indicator related to the additional administration of the use of high-energy radiation from x-rays, gamma rays, neutrons, and other sources to kill cancer cells and shrink tumors after the return of a disease.

(2650648)

Type: Particular kind of radiation therapy administered after the recurrence or progression of disease. (2759630)

Start Date: Date that additional radiation therapy began after the recurrence or progression of disease. (2759632)

Stop Date: Date that additional radiation therapy ended for the recurrence or progression of disease. (2759634)

Dosage: Text description of the total dose of radiation therapy administered to an individual expressed as a dosage amount and unit of measure (UOM). (2721441)

Fractions: The total number of radiation therapy sessions (fractions) which the patient has completed to receive the required radiation dose to primary treatment fields. (61465)

Tier 2 Clinical Data (Page 7 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 00E Additional treatment for tumor recurrence/ progression

Chemotherapy

Intravenous (IV)

Intra-peritoneal (IP)

IV and IP additional administration of chemotherapy after the return of a disease after a period of remission. (2650626)

Start Date: Date that additional chemotherapy ended for the recurrence of progression of disease. (2759815)

Drugs: Name of the additional chemotherapy agent administered to an individual after disease recurrence or progression. (2759817)

# of cycles: the total number of cycles (courses) administered to he patient of a protocol specified drug or therapy agent. (62590)

Total dose given: Agent total cumulative dose

(1515)

2:00F Additional treatment of tumor recurrence/progression

Immunotherapy

No

Yes additional administration of various treatment modalities that produce the desired therapeutic effect by means of change of hormone/hormones level after ther return of a disease after a period of remission or new disease. (2650646)

Start Date: Date that additional hormonal therapy began after the recurrence or progression of disease. (2759819)

Stop Date: Date that additional hormonal therapy ended for the recurrence or progression of disease. (2759821)

# of Cycles: The total number of cycles

(courses) administered to the patient of a protocol specified drug or therapy agent.

(62590)

Drugs Used: Name of the additional hormonal agent administered to an individual after disease recurrence or progression. (2759823)

Total dose given: Agent total cumulative dose

Tier 2 Clinical Data (Page 8 of 9)

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TSS Name:_________________ TSS Identifier #:

TSS Unique Patient # _____________________

2: 00G Additional treatment for tumor recurrence/ progression

Hormone therapy

No

Yes

Indicator: the yes/no indicator related to the additional administration of various treatment modalities that produce the desired therapeutic effect by means of change of hormone/hormones level after ther return of a disease after a period of remission or new disease. (2759828)

Start Date: Date that additional hormonal therapy began after the recurrence or progression of disease.

(2759830)

Stop Date: Date that additional hormonal therapy ended for the recurrence or progression of disease.

(2759832)

# of Cycles: The total number of cycles

(courses) administered to the patient of a protocol specified drug or therapy agent. (62590)

Drugs Used: Name of the additional hormonal agent administered to an individual after disease recurrence or progression. (2759834)

Total dose given: Agent total cumulative dose (1515)

2: 00H Additional treatment of tumor recurrence/progression

Targeted molecular therapy

No

Yes

Definitions and descriptions as previously described.

Comments:

Principal Investigator Signature Print Name M M D D Y Y

Tier 2 Clinical Data (Page 9 of 9)