Microscopic Findings (MI)

TOBA-53 - Getting issue details... STATUS

Example

This example shows different types of histopathological findings for 6 different animals.

Rows 1-2:	For these findings, the specimen consists of tissues from both the testis and the epididymis. Therefore, the list of tissues comprising the specimen becomes the SPEC value for each contributing tissue, noted by a slash, as is found in the controlled terminology list.
Row 2:	For this finding, the base pathological process is inflammation, and is recorded in MISTRESC. The term "acute" is recorded in MICHRON using the controlled CHRNCTY codelist term ACUTE.
Row 3:	For this finding, the specimen consists of skeletal muscle. The base pathological process is degeneration/regeneration and is represented in MISTRESC. The term "Myofiber" is recorded in MIRESMOD (SUPPMI example).
Row 4:	This is an example of a reason why a microscopic evaluation of the mammary gland specimen was not performed. Note that MIORRES is null and MISTAT is "NOT DONE", the reason for the specimen not being evaluated is entered in MIREASND.
Row 5:	This shows an example of a record where the specimen contained no pathologic process. A record should be included for every scheduled specimen that was without pathology. The controlled NONNEO term "UNREMARKABLE" is recorded in MISTRESC. Note: There is no MIRESCAT for "UNREMARKABLE" as there is no finding.
Row 6:	In this record, the finding was the cause of death; therefore, MIDTHREL is "Y" (Yes).
Row 7:	The base pathological process is hyperplasia, recorded into MISTRESC from the NONNEO controlled terminology list. The modifiers "endometrial" and "cystic" are recorded in MIRESMOD (SUPPMI example). Note that the 2 values for MIRESMOD are separated by a semicolon, as required in Section 6.3.8.
Row 8:	For this finding, a mass identified as mass 1 (MISPID="MASS 1") is observed on the left ovary (MILAT = "LEFT"). This mass is considered benign (MIRESCAT). Note that MISTRESC contains controlled terminology for the tumor, which may include term(s) similar to characteristics and/or distribution as part of the base pathological process.
Row 9:	This is an example of a malignant mass (MISPID = "MASS 2"). The malignancy of the mass is recorded as part of the original result (MIORRES) as well as the controlled term in MIRESCAT. This finding was not the cause of death of the subject (MIDTHREL= "N"). Note that MISTRESC contains only the finding without modifiers. This record is linked to row 11 (via the MIGRPID value of 1) to relate the primary tumor with its metastasis in another tissue. The tumor origin described in MIORRES ("Primary") is associated to the MI records using the supplemental qualifier MIRESMOD (SUPPMI example).
Row 10:	This shows an example of a metastasis found in the uterus. The primary site for this tumor is unknown, and the applicant decided to include row 13 ("SITE, UNCERTAIN PRIMARY") to represent the source tumor. This record is related to rows 12 and 13 via the MIGRPID value of 2.
Row 11:	This finding describes a mass (MISPID="MASS 3") that is a metastasis of a primary tumor, which is recorded in the original result (MIORRES). This specific finding did not cause the death of the animal (MIDTHREL="N"). This record is linked to row 9 via the MIGRPID value of 1 to relate the metastasis to the finding at the primary site identified for the tumor.
Row 12:	This record illustrates another metastasis row for the lymphoma found in multiple sites. This record is related to rows 10 and 13 via the MIGRPID value of 2.
Row 13:	This record is an example of how to represent an unknown primary site for the lymphoma found in the uterus and vagina (row 11). The applicant decided to include a row to represent the base tumor (TFSPEC="SITE, UNCERTAIN PRIMARY") related to the metastasis row via the MIGRPID of 2, and defining it as the cause of death (MIDTHREL="Y"). Note: The use of "SITE, UNCERTAIN PRIMARY" is applicant-specific; an alternative (based on how the data are collected) would be to exclude this row and only include rows for each site at which the tumor was found.
Rows 14-15:	These findings demonstrates an original result with modifiers, including a severity which is copied into MISEV. The base pathological process is entered into MISTRESC using the controlled terminology list and the remaining modifiers are recorded in MIRESMOD ("Mononuclear Cell" for line 14) and MIDISTR ("Multifocal" for line 15) in the SUPPMI example.
Rows 16-17:	These findings demonstrate the use of specimen location qualifiers of MIANTREG, MILAT, and MIDIR.
Row 18:	This finding demonstrates the use of finding qualifiers MICHRON, MIDISTR, and MIRESMOD, and the use of a semicolon to separate 2 terms in MIRESMOD (SUPPMI example).
Row 19:	This record is an example of an incidental malignant neoplasm in the liver that has not metastasized. The MIDTHREL is "N" because the tumor is incidental.

mi.xpt

Row	STUDYID	DOMAIN	USUBJID	MISEQ	MIGRPID	MISPID	MITESTCD	MITEST	MIORRES	MISTRESC	MICHRON	MIDISTR	MIRESCAT	MISTAT	MIREASND	MISPEC	MIANTREG	MILAT	MIDIR	MISEV	MIDTHREL	MIDTC	MIDY
1	123	MI	123-01	1			GHISTXQL	General Histopathologic Exam, Qual	Amyloidosis, grade 2	AMYLOID			NON-NEOPLASTIC			TESTIS/EPIDIDYMIS				MILD		2015-10-27	365
2	123	MI	123-01	2			GHISTXQL	General Histopathologic Exam, Qual	Inflammation, acute, grade 2	INFLAMMATION	ACUTE		NON-NEOPLASTIC			TESTIS/EPIDIDYMIS				MILD		2015-10-27	365
3	123	MI	123-01	3			GHISTXQL	General Histopathologic Exam, Qual	Degeneration/regeneration, myofiber, grade 4	DEGENERATION/ REGENERATION			NON-NEOPLASTIC			MUSCLE, SKELETAL				MARKED		2015-10-27	365
4	123	MI	123-01	4			GHISTXQL	General Histopathologic Exam, Qual						NOT DONE	Tissue not present for histologic examination no glandular tissue in section	GLAND, MAMMARY						2015-10-27	365
5	123	MI	123-01	5			GHISTXQL	General Histopathologic Exam, Qual	Normal	UNREMARKABLE						GLAND, PARATHYROID						2015-10-27	365
6	123	MI	123-02	6			GHISTXQL	General Histopathologic Exam, Qual	Inflammation, meninges, grade 5	INFLAMMATION			NON-NEOPLASTIC			BRAIN				SEVERE	Y	2015-05-15	200
7	123	MI	123-03	7			GHISTXQL	General Histopathologic Exam, Qual	Hyperplasia, endometrial cystic, grade 3	HYPERPLASIA			NON-NEOPLASTIC			UTERUS				MODERATE		2015-10-27	365
8	123	MI	123-03	8		MASS 1	GHISTXQL	General Histopathologic Exam, Qual	Adenoma: tubulostromal (benign neoplasm), left	ADENOMA, TUBULOSTROMAL, BENIGN			BENIGN			OVARY		LEFT			N	2015-10-27	365
9	123	MI	123-03	9	1	MASS 2	GHISTXQL	General Histopathologic Exam, Qual	Sarcoma: endometrial stromal (malignant neoplasm), Primary	STROMAL SARCOMA, ENDOMETRIAL, MALIGNANT			MALIGNANT			UTERUS					N	2015-10-27	365
10	123	MI	123-03	10	2		GHISTXQL	General Histopathologic Exam, Qual	Lymphoma: metastasis	LYMPHOMA, MALIGNANT			METASTATIC			UTERUS					U	2015-10-27	365
11	123	MI	123-03	11	1	MASS 3	GHISTXQL	General Histopathologic Exam, Qual	Sarcoma: metastasis; Uterus was the primary site	SARCOMA, MALIGNANT			METASTATIC			VAGINA					N	2015-10-27	365
12	123	MI	123-03	12	2		GHISTXQL	General Histopathologic Exam, Qual	Lymphoma: metastasis	LYMPHOMA, MALIGNANT			METASTATIC			VAGINA					U	2015-10-27	365
13	123	MI	123-03	13	2		GHISTXQL	General Histopathologic Exam, Qual	Lymphoma: multicentric	LYMPHOMA, MALIGNANT			MALIGNANT			SITE, UNCERTAIN PRIMARY					Y	2015-10-27	365
14	123	MI	123-04	14			GHISTXQL	General Histopathologic Exam, Qual	Infiltrate, mononuclear cell, grade 1	INFILTRATE			NON-NEOPLASTIC			MENINGES				MINIMAL		2015-10-27	365
15	123	MI	123-04	15			GHISTXQL	General Histopathologic Exam, Qual	Atrophy, multifocal, grade 2	ATROPHY		MULTIFOCAL	NON-NEOPLASTIC			TESTIS				MILD		2015-10-27	365
16	123	MI	123-04	16			GHISTXQL	General Histopathologic Exam, Qual	Intra-alveolar hemorrhage, right, grade 2	HEMORRHAGE			NON-NEOPLASTIC			LUNG	CRANIAL LOBE	RIGHT		MILD		2015-10-27	365
17	123	MI	123-04	17			GHISTXQL	General Histopathologic Exam, Qual	Cyst, right, anterior	CYST			NON-NEOPLASTIC			KIDNEY		RIGHT	ANTERIOR			2015-10-27	365
18	123	MI	123-05	18			GHISTXQL	General Histopathologic Exam, Qual	Inflammation, moderate, chronic, multifocal, mucosal, forestomach, grade 3	INFLAMMATION	CHRONIC	MULTIFOCAL	NON-NEOPLASTIC			STOMACH				MODERATE		2015-10-27	365
19	123	MI	123-06	19			GHISTXQL	General Histopathologic Exam, Qual	Hepatocellular carcinoma (malignant neoplasm without metastasis), incidental	CARCINOMA, HEPATOCELLULAR, MALIGNANT			MALIGNANT			LIVER					N	2015-10-07	345

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Dataset Wrapper Debug Message

Please add a row column to your dataset.

Rows 1-7: These rows show the supplemental qualifier records for the modifiers associated with the findings in Example 1. Via IDVAR and IDVARVAL, these records are linked to the MISEQ with the values 3, 7, 9, 13, 14, 16, and 18, respectively.

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suppmi.xpt

Row	STUDYID	RDOMAIN	USUBJID	IDVAR	IDVARVAL	QNAM	QLABEL	QVAL	QORIG	QEVAL
1	123	MI	123-01	MISEQ	3	MIRESMOD	Result Modifiers	Myofiber	COLLECTED	PATHOLOGIST
2	123	MI	123-03	MISEQ	7	MIRESMOD	Result Modifiers	Endometrial; Cystic	COLLECTED	PATHOLOGIST
3	123	MI	123-03	MISEQ	9	MIRESMOD	Result Modifiers	Primary	COLLECTED	PATHOLOGIST
4	123	MI	123-03	MISEQ	13	MIRESMOD	Result Modifiers	Multicentric	COLLECTED	PATHOLOGIST
5	123	MI	123-04	MISEQ	14	MIRESMOD	Result Modifiers	Mononuclear Cell	COLLECTED	PATHOLOGIST
6	123	MI	123-04	MISEQ	16	MIRESMOD	Result Modifiers	Intraalveolar	COLLECTED	PATHOLOGIST
7	123	MI	123-05	MISEQ	18	MIRESMOD	Result Modifiers	Mucosal; Forestomach	COLLECTED	PATHOLOGIST

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This comment table shows the representation of the comment that was included in MIORRES.

Row 1:	Demonstrates the representation of the comment that was included in MIORRES.
Row 2:	Shows how to represent a comment for an animal tissue that is not associated with any particular finding.

co.xpt

Row	STUDYID	DOMAIN	RDOMAIN	USUBJID	COSEQ	IDVAR	IDVARVAL	COVAL	CODTC
1	123	CO	MI	123-03	1	MISEQ	11	Site of primary neoplasm: UTERUS
2	123	CO	MI	123-01	2	MISPEC	GLAND, PARATHYROID	One of pair present

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Dataset Wrapper Debug Message

Please add a row column to your dataset.

Example

This example shows some multiple-base pathological processes, collected as if they were one finding.

The original descriptive text by the pathologist is repeated in the original result fields (MIORRES), because a finding should comprise only 1 base pathological process and its modifiers (severity, chronicity, or distribution, and the remaining in result modifiers as a supplemental qualifier record). Because there are 3 base processes described in MIORRES, there needs to be 3 records, each with 1 base process in MISTRESC.

mi.xpt

Row	STUDYID	DOMAIN	USUBJID	MISEQ	MIGRPID	MIREFID	MITESTCD	MITEST	MIORRES	MISTRESC	MICHRON	MISPEC	MISEV	MIDTC	MIDY
1	ABC	MI	ABC-101	1	1	101-A1	GHISTXQL	General Histopathologic Exam, Qual	Necrosis-hepatocytes in centrilobular area surrounded by slight acute inflammation with moderate hemorrhage	NECROSIS		LIVER		1991-05-17	91
2	ABC	MI	ABC-101	2	1	101-A1	GHISTXQL	General Histopathologic Exam, Qual	Necrosis-hepatocytes in centrilobular area surrounded by slight acute inflammation with moderate hemorrhage	INFLAMMATION	ACUTE	LIVER	MILD	1991-05-17	91
3	ABC	MI	ABC-101	3	1	101-A1	GHISTXQL	General Histopathologic Exam, Qual	Necrosis-hepatocytes in centrilobular area surrounded by slight acute inflammation with moderate hemorrhage	HEMORRHAGE		LIVER	MODERATE	1991-05-17	91

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This row shows the supplemental qualifier record for the modifiers associated with the findings in row 1.

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Row	STUDYID	RDOMAIN	USUBJID	IDVAR	IDVARVAL	QNAM	QLABEL	QVAL	QORIG	QEVAL
1	ABC	MI	ABC-101	MISEQ	3	MIRESMOD	Result Modifiers	Hepatocytes; Centrilobular	COLLECTED	PATHOLOGIST

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Example

This example shows the result of a histopathological evaluation of 2 injection sites on 1 animal.

Rows 1-2:	This shows 2 observations (base pathological processes) for injection site 1 (in FOCID). The finding is standardized when mapping to the controlled terminology in MISTRESC, MICHRON, MIDISTR, MISEV, and any additional modifiers in MIRESMOD (SUPPMI example).
Row 3:	A second injection site (in FOCID) on the same animal was also examined.

mi.xpt

Row	STUDYID	DOMAIN	USUBJID	FOCID	MISEQ	MITESTCD	MITEST	MIORRES	MISTRESC	MIDISTR	MISPEC	MISEV	MIDTC	MIDY
1	ABC	MI	ABC-101	Injection Site 1	1	GHISTXQL	General Histopathologic Exam, Qual	Subcutaneous Inflammation, Minimal	INFLAMMATION		SITE, INJECTION	MINIMAL	2015-10-27	42
2	ABC	MI	ABC-101	Injection Site 1	2	GHISTXQL	General Histopathologic Exam, Qual	Panniculus Muscle-Inflammation/Degeneration, Focal, Slight	INFLAMMATION/ DEGENERATION	FOCAL	SITE, INJECTION	MILD	2015-10-27	42
3	ABC	MI	ABC-101	Injection Site 2	3	GHISTXQL	General Histopathologic Exam, Qual	Subcutaneous Hemorrhage, Minimal	HEMORRHAGE		SITE, INJECTION	MINIMAL	2015-10-27	42

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Dataset Wrapper Debug Message

Please add a row column to your dataset.

This row shows the supplemental qualifier record for the modifiers associated with the findings in MI.

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Row	STUDYID	RDOMAIN	USUBJID	IDVAR	IDVARVAL	QNAM	QLABEL	QVAL	QORIG	QEVAL
1	ABC	MI	ABC-101	MISEQ	1	MIRESMOD	Result Modifiers	Subcutaneous	COLLECTED	PATHOLOGIST
2	ABC	MI	ABC-101	MISEQ	2	MIRESMOD	Result Modifiers	Panniculus Muscle	COLLECTED	PATHOLOGIST
3	ABC	MI	ABC-101	MISEQ	3	MIRESMOD	Result Modifiers	Subcutaneous	COLLECTED	PATHOLOGIST

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Example

This example shows how to tabulate data for a bilateral organ, where both sides were examined and only 1 result was reported.

One side was unremarkable and the other side had a finding. "UNREMARKABLE" was not tabulated; only the finding was included. Per schedule, both sides of the kidney were examined, so MILAT is "BOTH". Because the finding is reported for 1 unspecified side (unilateral), this is the result location, consequently tabulated as a result modifier (see MIRESMOD example below).

mi.xpt

Row	STUDYID	DOMAIN	USUBJID	MISEQ	MITESTCD	MITEST	MIORRES	MISTRESC	MICHRON	MIDISTR	MISPEC	MISPCCND	MISPCUFL	MILAT	MISEV	MIDTC	MIDY
1	ABC	MI	ABC-101	1	GHISTXQL	General Histopathologic Exam, Qual	Acute focal glomerular hemorrhage, unilateral	HEMORRHAGE	ACUTE	FOCAL	KIDNEY			BOTH		2015-10-27	42

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This row shows the supplemental qualifier record for the modifiers associated with the findings in MI.

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suppmi.xpt

Row	STUDYID	RDOMAIN	USUBJID	IDVAR	IDVARVAL	QNAM	QLABEL	QVAL	QORIG	QEVAL
1	ABC	MI	ABC-101	MISEQ	1	MIRESMOD	Result Modifiers	glomerular; unilateral	COLLECTED	PATHOLOGIST

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Microscopic Findings (MI)