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ajz-onc-crude-moore.sql
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ajz-onc-crude-moore.sql
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-- LUNG
SELECT TOP (200)
[patientsid]
,[Sta3n]
--,[OncologyPrimaryIEN],
,[Stagegroupclinical] --IMPORTANT
,[StageGroupingajcc] --IMPORTANT
,[SitegpX]
,[ICDOSite]
,[PrimarysiteX]
,[Histologyicdo3X] -- last good one?
--,[DateOfInpatientAdmission]
--,[DateOfInpatientDischarge]
,[DateDX]
--,[Palliativecare]
--,[Palliativecarefac]
--,[StagedByClinicalStage]
--,[PrimarySiteIEN]
--,[HistologyIcdo2IEN]
,[Histologyicdo2X]
--,[HistologyIcdo3IEN]
--,[GradedifferentiationidIEN]
--,[Gradedifferentiation]
--,[Gradepathsystem]
--,[Gradepathvalue]
--,[Tnmformassigned]
--,[TumorSize]
--,[TumorSizeextEvalCs]
--,[TumorSizeCs]
--,[LymphNodes]
--,[LymphNodesCs]
--,[RegionalLymphNodesPositive]
--,[RegNodesEvalCs]
--,[RegionalLymphNodesExamined]
--,[SiteOfDistantMetastasis1]
--,[SiteOfDistantMetastasis2]
--,[SiteOfDistantMetastasis3]
--,[MetsAtDxCs]
--,[Metsatdxbone]
--,[Metsatdxbrain]
--,[Metsatdxliver]
--,[Metsatdxlung]
--,[MetsEvalCs]
,[SeerSummaryStage2000]
,[AjccStagingBasis]
,[ClinicalT]
,[ClinicalN]
,[ClinicalM]
--,[AutomaticStagingOverridden]
,[OtherstagingsystemidIEN]
,[Otherstagingsystem]
--,[Tnmformcompleted]
--,[PerformanceStatus]
--,[SurgicalDxstagingProc]
--,[SurgeryOfPrimaryR]
--,[SurgicalDxstagingProcDate]
--,[SurgDxstagingProcFac]
--,[SurgDxstagingProcFacDate]
,[PhysiciansStage]
--,[PhysicianStagingIEN]
--,[PhysicianstagingX] --doctor name
,[PathologicT]
,[PathologicN]
,[Pathologicm]
,[Stagegrouppathologic]
--,[Stagedbypathologicstage]
,[Otherstagegroup]
,[Stagedbyotherstage]
--,[Censustract]
,[Derivedajcc6t]
,[Derivedajcc7t]
,[Derivedajcc6tdescriptor]
,[Derivedajcc7tdescriptor]
,[Derivedajcc6n]
,[Derivedajcc7n]
,[Derivedajcc6ndescriptor]
,[Derivedajcc7ndescriptor]
,[Derivedajcc6m]
,[Derivedajcc7m]
,[Derivedajcc6mdescriptor]
,[Derivedajcc7mdescriptor]
,[Derivedajcc6stagegroup]
,[Derivedajcc7stagegroup]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%'
-- MUCH MORE COMPACT CODE
SELECT TOP (200)
[patientsid],[Sta3n],[Stagegroupclinical] ,[StageGroupingajcc] ,[SitegpX],[ICDOSite],[PrimarysiteX],[Histologyicdo3X] -- last good one?
,[DateDX],[Histologyicdo2X],[SeerSummaryStage2000]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
-- COUNTS
select count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
-- 71583
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
--62466
-- BY CLINICAL
SELECT count(*) as n, [Stagegroupclinical]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
--and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
group by Stagegroupclinical
order by n desc
/*
DON'T USE ME. THESE DATA INCLUDE SMALL CELL.
n Stagegroupclinical
14566 1A
14138 4
11394 NULL
6902 3A
5364 99
4890 1B
3984 3B
2486 2B
2317 2A
1205 1A2
1054 4B
839 4A
829 1
409 88
301 1A1
237 OC
182 2
162 3
137 0
121 3C
37 4C
18 0C
3 0IS
2 1C
2 2A2
1 4A2
1 3C1
1 1B2
1 1S
*/
-- BY AJCC INCLUDING SMALL CELL
SELECT count(*) as n, Stagegroupingajcc
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%'
group by Stagegroupingajcc
order by n desc
/*
n Stagegroupingajcc
22712 I
16199 IV
11706 III
11012 NULL
6271 II
3055 Unk/Uns
407 NA
221 0
I and II = 28,983
0 I II = 29204
III and IV = 27,905
Ratio 1.05:1
Or late/total = 0.489
Null unk na = 14474
57109 staged. Tot 71583. Checks out perfectly.
*/
-- BY AJCC EXCLUDE SMALL CELL
-- GOOD STUFF NEXT STATEMENT
SELECT count(*) as n, Stagegroupingajcc
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
group by Stagegroupingajcc
order by n desc
/*
n Stagegroupingajcc
21749 I
12729 IV
10144 III
8877 NULL
5852 II
2645 Unk/Uns
258 NA
212 0
*/
-- EARLY
SELECT count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
and (Stagegroupingajcc = 'I' or Stagegroupingajcc = 'II' or Stagegroupingajcc = '0')
--27813
--LATE
SELECT count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
and (Stagegroupingajcc = 'III' or Stagegroupingajcc = 'IV')
--22873
-------- COLON --------
SELECT TOP (200)
[patientsid],[Sta3n],[Stagegroupclinical] ,[StageGroupingajcc] ,[SitegpX],[ICDOSite],[PrimarysiteX],[Histologyicdo3X] -- last good one?
,[DateDX],[Histologyicdo2X],[SeerSummaryStage2000]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
--and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
select count(*) as n, [Histologyicdo3X]
from [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
group by Histologyicdo3X
order by n desc
-- 128 rows
/*
23383 ADENOCARCINOMA, NOS
1869 MUCINOUS ADENOCARCINOMA
1784 ADENOCARCINOMA ADENOMATOUS IN POLYP
1763 ADENOCARCINOMA IN TUBULOVILLOUS ADENOMA
1192 ADENOCA IN SITU IN TUBULOVILLOUS ADENOMA
1127 ADENOCARCINOMA IN SITU IN ADENOMATOUS POLYP
840 ADENOCARCINOMA IN SITU, NOS
806 CARCINOMA IN SITU, NOS
458 CARCINOID TUMOR, NOS
420 ADENOCARCINOMA IN VILLOUS ADENOMA
369 NULL
336 CARCINOMA, NOS
271 MUCIN-PRODUCING ADENOCARCINOMA
260 SIGNET RING CELL CARCINOMA
242 NEOPLASM, MALIGNANT
218 ADENOCARCINOMA IN SITU IN VILLOUS ADENOMA
211 NEUROENDOCRINE CARCINOMA, NOS
89 ATYPICAL ADENOMA
88 GOBLET CELL CARCINOID
79 MALIGNANT LYMPHOMA, LRGE B-CELL, DIFFUSE, NOS
57 CARCINOID TUMOR OF UNCERTAIN MALIG POTENTIAL
52 MANTLE CELL LYMPHOMA
46 ADENOCARCINOMA WITH MIXED SUBTYPES
45 MARGINAL ZONE B-CELL LYMPHOMA, NOS
39 MEDULLARY CARCINOMA, NOS *** 1%
33 TUBULAR ADENOCARCINOMA IN SITU *** <1%
32 VILLOUS ADENOMA, NOS
32 TUMOR CELLS, MALIGNANT
31 TUBULAR ADENOCARCINOMA
28 COMPOSITE CARCINOID
28 GASTROINTESTINAL STROMAL SARCOMA
28 ADENOMA, NOS
*/
-- bad ones:
/*
458 CARCINOID TUMOR, NOS
211 NEUROENDOCRINE CARCINOMA, NOS
89 ATYPICAL ADENOMA
88 GOBLET CELL CARCINOID
79 MALIGNANT LYMPHOMA, LRGE B-CELL, DIFFUSE, NOS
57 CARCINOID TUMOR OF UNCERTAIN MALIG POTENTIAL
52 MANTLE CELL LYMPHOMA
45 MARGINAL ZONE B-CELL LYMPHOMA, NOS
32 VILLOUS ADENOMA, NOS
28 COMPOSITE CARCINOID
28 GASTROINTESTINAL STROMAL SARCOMA
28 ADENOMA, NOS
*/
--false pos examples
SELECT TOP (200)
[patientsid],[Sta3n],[Stagegroupclinical] ,[StageGroupingajcc] ,[SitegpX],[ICDOSite],[PrimarysiteX],[Histologyicdo3X] -- last good one?
,[DateDX],[Histologyicdo2X],[SeerSummaryStage2000]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and Histologyicdo3X like 'carcinoid%'
SELECT count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
--36705
SELECT count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like 'carcinoid%' or
Histologyicdo3X like 'neuro%' or
Histologyicdo3X like 'atypical adenom%' or
Histologyicdo3X like 'goblet cell carcinoi%' or
Histologyicdo3X like 'malignant lymp%' or
Histologyicdo3X like 'mantle%' or
Histologyicdo3X like 'marginal%' or
Histologyicdo3X like 'villous adenom%' or
Histologyicdo3X like 'composite carcinoi%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like 'adenoma%')
--35089
select count(*) as n, [Histologyicdo3X]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like 'carcinoid%' or
Histologyicdo3X like 'neuro%' or
Histologyicdo3X like 'atypical adenom%' or
Histologyicdo3X like 'goblet cell carcinoi%' or
Histologyicdo3X like 'malignant lymp%' or
Histologyicdo3X like 'mantle%' or
Histologyicdo3X like 'marginal%' or
Histologyicdo3X like 'villous adenom%' or
Histologyicdo3X like 'composite carcinoi%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like 'adenoma%')
group by Histologyicdo3X
order by n desc
-- 104 rows
-- double percent
select count(*) as n, [Histologyicdo3X]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like '%carcinoid%' or
Histologyicdo3X like '%neuro%' or
Histologyicdo3X like '%adenoma%' or
Histologyicdo3X like '%lymph%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like '%sarcoma%')
group by Histologyicdo3X
order by n desc
-- 66 rows, performs OK.
/* DONE REFINING WHERE CLAUSE */
select TOP (200)
[patientsid],[Sta3n],[Stagegroupclinical] ,[StageGroupingajcc] ,[SitegpX],[ICDOSite],[PrimarysiteX],[Histologyicdo3X] -- last good one?
,[DateDX],[Histologyicdo2X],[SeerSummaryStage2000]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like '%carcinoid%' or
Histologyicdo3X like '%neuro%' or
Histologyicdo3X like '%adenoma%' or
Histologyicdo3X like '%lymph%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like '%sarcoma%')
-- GOOD STUFF NEXT STATEMENT
select count(*) as n, [StageGroupingajcc]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like '%carcinoid%' or
Histologyicdo3X like '%neuro%' or
Histologyicdo3X like '%adenoma%' or
Histologyicdo3X like '%lymph%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like '%sarcoma%')
group by StageGroupingajcc
order by n desc
/*
n StageGroupingajcc
6781 II
6699 I
5897 III
2790 IV
2469 NULL
1999 Unk/Uns
1738 0
28 NA
*/
/************************ LOOK AT ICD CODES ************************/
-- YOU CAN SKIP THIS INITIAL EXPLORATION AND GO DO WHERE IT SAYS "--RUN"
-- Expect C18 colon, C19 rectosig, C20 rectum
select top 10
icd10sid, icdien, sta3n, ICD10Code
from CDWWork.dim.ICD10
where ICD10Code like 'c18%'
select count(*)
from CDWWork.dim.ICD10
where ICD10Code like 'c18%' --1300
or icd10code like 'c19%' or ICD10Code like 'c20%' --1560 for all 3 codes
--lung
-- C34.0 main bronch, .1 upper, .2 middle, 3 lower, 8 other, 90 unspec
-- really can just do C34*.
select top 100
icd10sid, icdien, sta3n, ICD10Code
from CDWWork.dim.ICD10
where ICD10Code like 'c34%'
select count(*)
from CDWWork.dim.ICD10
where ICD10Code like 'c34%' --2080
and Sta3n = 580 -- 16
select * from CDWWork.dim.ICD10 where ICD10Code like 'c34%' and Sta3n = 580
-- temp tables
drop table #ajz_lungca_outpats
select top 100
patientsid, VisitDateTime, PrimarySecondary, ICD10Code
into #ajz_lungca_outpats
from ORD_Singh_202001030D.src.Outpat_VDiagnosis as outpa
inner join
cdwwork.dim.icd10 as icd
on icd.icd10sid = outpa.icd10sid
where outpa.sta3n=580 and outpa.ICD10SID > 0 and icd.ICD10Code like 'c34%'
select count(*) as N into #ajz_deleteme
from ORD_Singh_202001030D.src.Outpat_VDiagnosis as outpa
inner join
cdwwork.dim.icd10 as icd
on icd.icd10sid = outpa.icd10sid
where outpa.sta3n=580 and outpa.ICD10SID > 0 and icd.ICD10Code like 'c34%'
-- 26996 diagnoses in HOU for lung CA, in unk. no. of pts.
--tempdb.dbp.#blah
select * from #ajz_deleteme
select * from #ajz_lungca_outpats
select distinct patientsid from #ajz_lungca_outpats -- SELECT TOP 10 visits but 8 PatientSID. Or 100:50.
-- join with registry
select distinct outpa.patientsid, outpa.PrimarySecondary, outpa.ICD10Code
,reg.[Stagegroupclinical] ,reg.[StageGroupingajcc] ,reg.[SitegpX],reg.[ICDOSite],reg.[PrimarysiteX],reg.[Histologyicdo3X]
,reg.[DateDX],reg.[Histologyicdo2X],reg.[SeerSummaryStage2000]
--drop visitDateTime
from #ajz_lungca_outpats as outpa
left join
[ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as reg
on outpa.PatientSID = reg.PatientSID
order by patientsid
--narrow down more.
select distinct outpa.patientsid, outpa.ICD10Code
,reg.datedx
,reg.[Stagegroupclinical] ,reg.[StageGroupingajcc] ,reg.[SitegpX],reg.[ICDOSite],reg.[PrimarysiteX],reg.[Histologyicdo3X]
,reg.[SeerSummaryStage2000]
from #ajz_lungca_outpats as outpa
left join
[ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as reg
on outpa.PatientSID = reg.PatientSID
order by patientsid, DateDX
--insight: people may be in there with more than 1 datedx.
--narrower.
select distinct outpa.patientsid
,reg.[SitegpX],reg.[ICDOSite] --reg.[PrimarysiteX] --reg.[Histologyicdo3X] is too granular. So is reg.[SeerSummaryStage2000]
, (case when reg.SitegpX like 'lung%' then 'Y' else NULL end) as is_lung
from #ajz_lungca_outpats as outpa
left join
[ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as reg
on outpa.PatientSID = reg.PatientSID
order by patientsid
--If include histologyICDO3X: 14 rows instead of 19
-- Drop histology and seersummary: 12 rows
-- drop primarySiteX: 11 rows
/* That was nice. Now increase the number in the temp table. */
-- 100 outpat dx --> 65 rows. (?)
-- GOOD STUFF NEXT STATEMENTS
--RUN
drop table #ajz_lungca_sidonly
select distinct top 10000 --10000 = 5 sec = 1544 patientSID
patientsid
into #ajz_lungca_sidonly
from ORD_Singh_202001030D.src.Outpat_VDiagnosis as outpa
inner join
cdwwork.dim.icd10 as icd
on icd.icd10sid = outpa.icd10sid
where outpa.sta3n=580 and outpa.ICD10SID > 0 and icd.ICD10Code like 'c34%'
--RUN
drop table #ajz_icd_reg
select distinct lung.patientsid ,reg.[SitegpX],reg.[ICDOSite]
into #ajz_icd_reg
from #ajz_lungca_sidonly as lung
left join
[ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as reg
on lung.PatientSID = reg.PatientSID
order by patientsid -- 1931 rows
select top 10 * from #ajz_icd_reg
select distinct patientsid from #ajz_icd_reg
where SitegpX like 'lung%'
-- 96/100 ! Surprisingly most are in registry under LUNG.
-- or 1176 / 1931, when we used 10,000 as our base param.
-- 60.9%
-- Bear in mind, this is anyone with ONE OR MORE visit for lung cancer, using OUTPATIENT VISITS ONLY.
-- Not even the stringent criterion of TWO OR MORE visits with ICD tag for lung cancer.
/******** LUNG NULL/UNK STAGE ********/
SELECT TOP (200)
[patientsid],[StageGroupingajcc],[DateDX], [Sta3n],[Stagegroupclinical] ,[SitegpX],[ICDOSite],[PrimarysiteX],[Histologyicdo3X]
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
and not HistologyIcdo3X like 'lymph%'
and (StageGroupingajcc like 'Unk%' or StageGroupingajcc like 'NA%' or StageGroupingajcc is null)
-- TODO : exclude lymphoma above.
-- "Unk/Uns" is one string and "NA" is another
-- deleted: choose one patientsid for each type of odd stageGroupingAJCC
select top 200 t.TIUDocumentSID, t.sta3n, t.TIUDocumentDefinitionSID, patientsid, EpisodeBeginDateTime, DocumentSubject,
d.TIUDocumentDefinition
from ORD_Singh_202001030D.[Src].[TIU_TIUDocument] as t
inner join cdwwork.dim.TIUDocumentDefinition as d
on t.TIUDocumentDefinitionSID = d.TIUDocumentDefinitionSID
-- no reportText??
select * from ORD_Singh_202001030D.INFORMATION_SCHEMA.COLUMNS
where COLUMN_NAME like 'reporttext%'
-- ah ha! See STIUNotes_TIUDocument_8925 and SPatientText_RadiologyReportText
select top 200 t.TIUDocumentSID, t.sta3n, t.TIUDocumentDefinitionSID, patientsid, EpisodeBeginDateTime, DocumentSubject,reporttext,
d.TIUDocumentDefinition
from ORD_Singh_202001030D.[Src].STIUNotes_TIUDocument_8925 as t
inner join cdwwork.dim.TIUDocumentDefinition as d
on t.TIUDocumentDefinitionSID = d.TIUDocumentDefinitionSID
-- deleted : select by patientsid
/*nursing onc for patient "NA"
**** recurrent lung adenoca
patient "NULL"
**** dx 2018 IIIA recur 2019 met
*/
select t.TIUDocumentDefinitionSID, patientsid, EpisodeBeginDateTime, reporttext,
d.TIUDocumentDefinition
from ORD_Singh_202001030D.[Src].STIUNotes_TIUDocument_8925 as t
inner join cdwwork.dim.TIUDocumentDefinition as d
on t.TIUDocumentDefinitionSID = d.TIUDocumentDefinitionSID
where PatientSID in (000000) -- deleted : select by patientsid
order by t.EpisodeBeginDateTime
/*Unk/Uns
new fdg avid rll r hilar lung lesions. pet ct non va but ordered by va. preceded by ct chest.
ct evidently done for inc cough sputum h/o copd c/f pna
*/
/******** Assess stability of measures 2020-01-28 ********/
SELECT sta3n, Stagegroupingajcc, count(*) as n
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
group by sta3n, Stagegroupingajcc
order by sta3n, StageGroupingajcc
-- 876 rows
select sta3n, StageGroupingajcc, count(*) as n
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like '%carcinoid%' or
Histologyicdo3X like '%neuro%' or
Histologyicdo3X like '%adenoma%' or
Histologyicdo3X like '%lymph%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like '%sarcoma%')
group by sta3n, StageGroupingajcc
order by sta3n, StageGroupingajcc
--845 rows
/******** development review chart pull for preeti ********/
select count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5]
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
--67923 Lung
select * from (
SELECT
onc.[PatientSID],onc.[Sta3n],onc.[Stagegroupclinical] , onc.[StageGroupingajcc] , onc.[SitegpX], onc.[ICDOSite], onc.[PrimarysiteX], onc.[Histologyicdo3X]
, onc.[DateDX],onc.[Histologyicdo2X],onc.[SeerSummaryStage2000]
, spat.PatientName, spat.PatientSSN, spat.BirthDateTime
, ROW_NUMBER() over (order by onc.patientsid) as patientsid_rank
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as onc
left join ORD_Singh_202001030D.src.SPatient_SPatient as spat
on onc.PatientSID = spat.PatientSID
where (SitegpX like 'lung%' or ICDOSite like 'lung%' or PrimarysiteX like 'lung%')
and not HistologyIcdo3X like 'small%' and not HistologyIcdo3X like 'carcinoid%' and not HistologyIcdo3X like 'neuro%'
) as x
where patientsid_rank = 31510 --these came from random.org and are not identifiers
or patientsid_rank = 47181
or patientsid_rank = 4020
or patientsid_rank = 65617
or patientsid_rank = 29199
or patientsid_rank = 54735
or patientsid_rank = 44681
or patientsid_rank = 26228
or patientsid_rank = 12608
or patientsid_rank = 13719
select count(*)
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as onc
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like '%carcinoid%' or
Histologyicdo3X like '%neuro%' or
Histologyicdo3X like '%adenoma%' or
Histologyicdo3X like '%lymph%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like '%sarcoma%')
--29878 colon
select * from (
select
onc.[PatientSID],onc.[Sta3n],onc.[Stagegroupclinical] , onc.[StageGroupingajcc] , onc.[SitegpX], onc.[ICDOSite], onc.[PrimarysiteX], onc.[Histologyicdo3X]
, onc.[DateDX],onc.[Histologyicdo2X],onc.[SeerSummaryStage2000]
, spat.PatientName, spat.PatientSSN, spat.BirthDateTime
, ROW_NUMBER() over (order by onc.patientsid) as patientsid_rank
FROM [ORD_Singh_202001030D].[Src].[Oncology_Oncology_Primary_165_5] as onc
left join ORD_Singh_202001030D.src.SPatient_SPatient as spat
on onc.PatientSID = spat.PatientSID
where (SitegpX like 'colo%' or ICDOSite like 'colo%' or PrimarysiteX like 'colo%')
and not (Histologyicdo3X like '%carcinoid%' or
Histologyicdo3X like '%neuro%' or
Histologyicdo3X like '%adenoma%' or
Histologyicdo3X like '%lymph%' or
Histologyicdo3X like 'gastrointestinal strom%' or
Histologyicdo3X like '%sarcoma%')
) as x
where patientsid_rank = 19667 --these came from random.org and are not identifiers
or patientsid_rank = 6109
or patientsid_rank = 19502
or patientsid_rank = 16965
or patientsid_rank = 13910
or patientsid_rank = 26319
or patientsid_rank = 24578
or patientsid_rank = 10772
or patientsid_rank = 9758
or patientsid_rank = 20058