callahantiff commented 5 years ago

Creating as a separate issue to break-up issue #2

Finalizing the Steroid-Induced Osteonecrosis Phenotype

Case Criteria:

Presence of ANY corticosteroid (no minimum dose IV, IM or PO ≥ 14 days cumulative) (medication string)

NOT presence of Alcohol Abuse (ICD9 code)

NOT presence of Sickle Cell (ICD9 code)

NOT presence of Gaucher (ICD9 code)

NOT presence of Legge-Calve-Perthes (ICD9 code)

NOT presence of HIV + (Exclude if value ≠ “undetectable” or is NULL) (ICD9 code) (medication string)

NOT presence of Organ Transplant (ICD9 code) (CPT code)

NOT presence of specific keywords related to comorbidities (keywords)

Presence of aseptic necrosis of bone (query window from steroid initiation to termination + 1 yr) (ICD9 code) OR

Presence of specific keywords suggestive of osteonecrosis (keywords)

Control Criteria:

Presence of ANY corticosteroid (no minimum dose IV, IM or PO ≥ 14 days cumulative) (medication string)

NOT presence of bisphosphonates (pulled list from Wikipedia)

NOT presence of Alcohol Abuse (ICD9 code)

NOT presence of Sickle Cell (ICD9 code)

NOT presence of Gaucher (ICD9 code)

NOT presence of Legge-Calve-Perthes (ICD9 code)

NOT presence of HIV + (Exclude if value ≠ “undetectable” or is NULL) (ICD9 code) (medication string) (lab code)

NOT presence of Organ Transplant (ICD9 code) (CPT code)

NOT presence of specific keywords suggestive of osteonecrosis (keywords)

Questions:

[x] Am I missing any bisphosponates?
- Etidronate
- Clodronate
- Tiludronate
- Nitrogenous
- Neridronate
- Olpadronate
- Alendronate
- Ibandronate
- Risedronate
- Zoledronate
- Pamidronate
- Didronel
- Bonefos
- Loron
- Aredia
- Zometa
- Aclasta
- Actonel
- Fosamax
- Skelid
- Nerixia
- Boniva - US
- Bonviva - Asia
- pamidronate disodium

[x] Are these the best LOINC terms for the following concepts?
- HIV-1: LOINC 29893-5
- HIVQnt: LOINC 20447-9 or LOINC 29541-0
- HIV-1_RNA_Ultraquant: LOINC 20447-9
- HIV-1RNA(LOG_10): LOINC 29541-0

@tdbennett, can you please advise on these questions?

tdbennett commented 5 years ago

https://www.whocc.no/atc_ddd_index/?showdescription=yes&code=M05BA

for bisphosphanates

tdbennett commented 5 years ago

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=2ahUKEwjn1-D8_pXhAhUKtIMKHfwnD08QFjAEegQIABAC&url=https%3A%2F%2Fwww.cdc.gov%2Fhiv%2Fxls%2Fguidelines%2Fcdc-hiv-diagnostic-tests-loinc-map.xlsx&usg=AOvVaw35AoTANQ24dhZ8xHR1d0eG

for HIV and LOINC. "Endorsed" by CDC

callahantiff commented 5 years ago

Thanks Tell!

[x] Just to clarify, are you saying that I should ONLY use the following for bisphosphanates?
etidronic acid
clodronic acid
pamidronic acid
alendronic acid
tiludronic acid
ibandronic acid
risedronic acid
zoledronic acid

[x] For HIV LOINC labs:

Using the CDC spreadsheet cross-referenced by what we have data for yields the following (I'm not sure we want row 2):

Row	LOINC
1	20447-9: HIV 1 RNA [#/volume] (viral load) in Serum or Plasma by NAA with probe detection
2	56888-1: HIV 1+2 Ab+HIV1 p24 Ag [Presence] in Serum or Plasma by Immunoassay
3	69668-2: HIV 1 and 2 Ab [Identifier] in Serum or Plasma by Rapid immunoassay

That being said, we also have data for the following labs that seem very relevant, yet are not included in this spreadsheet:

Row	LOINC
4	14092-1: HIV 1 Ab [Presence] in Serum by Immunofluorescence
5	21333-0: HIV 1 RNA [#/volume] in Serum
6	25836-8: HIV 1 RNA [#/volume] (viral load) in Unspecified specimen by NAA with probe detection

Which labs should we move forward with?

tdbennett commented 5 years ago

1) re: bisphosphanates, no. You probably know this, but -onate = -onic acid. Also, whatever the trade name equivalents are for those.

2) We should probably use all 6. Rows 2,3,4 are all yes/no and seem good to use. If I read the phenotype at the top correctly, we exclude patients if their viral load (rows 1,5,6) ~= undetectable. Is that how you read it?

callahantiff commented 5 years ago

re: bisphosphanates, no. You probably know this, but -onate = -onic acid. Also, whatever the trade name equivalents are for those.

Response:
OK, thanks! This is what I am including (using ChEMBL as the resource to link to trade names):

etidronic acid --> DIDRONEL, DIDRONEL IV, DIDRONEL PMO, ETIDRONATE DISODIUM
clodronic acid --> BONEFOS
pamidronic acid --> Aredia Pamidronate, disodium
alendronic acid --> BINOSTO, FOSAMAX
tiludronic acid --> SKELID
ibandronic acid --> BONDRONAT, BONVIVA, IASIBON, QUODIXOR
risedronic acid --> ACTONEL, ATELVIA, RISEDRONATE SODIUM
zoledronic acid --> ACLASTA, RECLAST, ZERLINDA, ZOLEDRONIC ACID, ZOMETA
1. We should probably use all 6. Rows 2,3,4 are all yes/no and seem good to use. If I read the phenotype at the top correctly, we exclude patients if their viral load (rows 1,5,6) ~= undetectable. Is that how you read it?
Response:
OK, that sounds good. I will note that we are to use all of the labs shown in the table above.

callahantiff commented 5 years ago

@trinklek, I am reviewing the source_strings for this phenotype (definition here) and found that one did not return a match: "aredia pamidronate". I found the following from CHEMBL:

Should I search for the synonyms listed in this table?

callahantiff commented 5 years ago

@jwyrwa , I am reviewing the source_strings for this phenotype (definition here) and found that the following strings did not return a match to a source_code in our database:

[x] bone-marrow transplant. Are there alternative phrases or synonyms that I should investigate?
[x] osteochondritis dessicans. Are there alternative phrases or synonyms that I should investigate?
[ ] HIV3rd. Are there alternative phrases or synonyms that I should investigate?

trinklek commented 5 years ago

@trinklek, I am reviewing the source_strings for this phenotype (definition here) and found that one did not return a match: "aredia pamidronate". I found the following from CHEMBL:

Should I search for the synonyms listed in this table?

Yes, these synonyms are accurate. I am surprised to see a string with both the brand and generic in it. I will be interested to see if this happens frequently.

callahantiff commented 5 years ago

@trinklek, I am reviewing the source_strings for this phenotype (definition here) and found that one did not return a match: "aredia pamidronate". I found the following from CHEMBL: Should I search for the synonyms listed in this table?

Yes, these synonyms are accurate. I am surprised to see a string with both the brand and generic in it. I will be interested to see if this happens frequently.

@trinklek, perfect. I will search the strings as they appear as well as separately to ensure we get the best coverage. Thank you!

jwyrwa commented 5 years ago

@callahantiff

For #1, I wonder if leaving the "-" out makes a difference. If not, BMT might work.

I believe #2 is misspelled. Dissecans vs dessicans.

3, is the 3rd in reference to which version of the test was used? If so, just going with HIV seems appropriate.

callahantiff commented 5 years ago

@jwyrwa -- This is very helpful, thank you!

@callahantiff

For #1, I wonder if leaving the "-" out makes a difference. If not, BMT might work.

Great suggestions, both solutions were tried and did not return a match. I also tried "marrow transplant". Maybe it's OK that this didn't match and we are covered with the ICD9cm and CPT codes the author supplied (see below)? Unless, you think something is missing?

Vocabulary	Code	Code Label
ICD9CM	"V58.44"	Aftercare following organ transplant
ICD9CM	"V42.81"	Bone marrow replaced by transplant
ICD9CM	"996.89"	Complications of other specified transplanted organ
ICD9CM	"996.85"	Complications of transplanted bone marrow
ICD9CM	"996.83"	Complications of transplanted heart
ICD9CM	"996.87"	Complications of transplanted intestine
ICD9CM	"996.81"	Complications of transplanted kidney
ICD9CM	"996.82"	Complications of transplanted liver
ICD9CM	"996.84"	Complications of transplanted lung
ICD9CM	"996.8"	Complications of transplanted organ
ICD9CM	"996.80"	Complications of transplanted organ, unspecified
ICD9CM	"996.86"	Complications of transplanted pancreas
ICD9CM	"V42.1"	Heart replaced by transplant
ICD9CM	"V42.0"	Kidney replaced by transplant
ICD9CM	"V42.7"	Liver replaced by transplant
ICD9CM	"V42.6"	Lung replaced by transplant
ICD9CM	"V42"	Organ or tissue replaced by transplant
ICD9CM	"V42.84"	Organ or tissue replaced by transplant, intestines
ICD9CM	"V42.8"	Other specified organ or tissue replaced by transplant
ICD9CM	"V42.89"	Other specified organ or tissue replaced by transplant
ICD9CM	"V42.83"	Pancreas replaced by transplant
ICD9CM	"V42.82"	Peripheral stem cells replaced by transplant
ICD9CM	"V42.9"	Unspecified organ or tissue replaced by transplant
CPT4	"S2103"	adrenal tissue transplant
CPT4	"580"	anesthesia for heart transplant or heart/lung transplant
CPT4	"38240"	bone marrow or blood-derived peripheral stem cell transplantation;
CPT4	"38241"	bone marrow or blood-derived peripheral stem cell transplantation;
CPT4	"38242"	bone marrow or blood-derived peripheral stem cell transplantation;
CPT4	"0085t"	breath test for heart transplant rejection
CPT4	"33945p"	heart transplant, w/wo re
CPT4	"33945"	heart transplant, with or without recipient cardiectomy
CPT4	"33635-50"	heart-lung transplant w/
CPT4	"33935"	heart-lung transplant with recipient cardiectomy-pneumonectomy
CPT4	"44135"	intestinal allotransplantation; from cadaver donor
CPT4	"44136"	intestinal allotransplantation; from living donor
CPT4	"47136"	liver allotransplantation; heterotopic, partial or whole, from cadaver
CPT4	"47135"	liver allotransplantation; orthotopic, partial or whole, from cadaver or
CPT4	"S2060"	lobar lung transplantatio
CPT4	"32854"	lung transplant, double (bilateral sequential or en bloc); with
CPT4	"32853"	lung transplant, double (bilateral sequential or en bloc); without
CPT4	"32851p"	lung transplant, single
CPT4	"32852p"	lung transplant, single
CPT4	"32852"	lung transplant, single; with cardiopulmonary bypass
CPT4	"32851"	lung transplant, single; without cardiopulmonary bypass
CPT4	"48160"	pancreatectomy, total or subtotal, with autologous transplantation of
CPT4	"44137"	removal of transplanted intestinal allograft, complete
CPT4	"48556"	removal of transplanted pancreatic allograft
CPT4	"50370"	removal of transplanted renal allograft
CPT4	"50365"	renal allotransplantation, implantation of graft; with recipient
CPT4	"50360"	renal allotransplantation, implantation of graft; without recipient
CPT4	"50380"	renal autotransplantation, reimplantation of kidney
CPT4	"S2054"	transplantation multivisc
CPT4	"48554"	transplantation of pancreatic allograft
CPT4	"76776"	ultrasound, transplanted kidney, real time and duplex doppler with image

I believe #2 is misspelled. Dissecans vs dessicans.

OK, I was legitimately worried that the typo was my fault. Turns, out that "dessicans" is how the phenotype author spelled it and I just copied the spelling mistake. Sort of ironic that even word tried to highlight the typo! 😃

I will run again with the correct spelling and see if we get anything else.

3, is the 3rd in reference to which version of the test was used? If so, just going with HIV seems appropriate.

Fair question, unfortunately, the only information I am given is this:

Earlier this year, it was suggested that we focus on the labs listed in a specific CDC Resource and here you can see what I found form digging it through it and querying our data sources. What are your thoughts?

callahantiff commented 5 years ago

@jwyrwa, I missed one sorry! Any alternative strategies for searching "bowel transplant"? I was thinking I could try "intestine transplant" and "intestinal transplant"?

tdbennett commented 5 years ago

HSCT - hematopoietic stem cell transplant

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726064/

On May 28, 2019, at 7:29 PM, Tiffany J. Callahan notifications@github.com wrote:

@callahantiff https://github.com/callahantiff For #1 https://github.com/callahantiff/PheKnowVec/issues/1, I wonder if leaving the "-" out makes a difference. If not, BMT might work.

Great suggestions, both solutions were tried and did not return a match. I also tried "marrow transplant". Maybe it's OK that this didn't match and we are covered with the ICD9cm and CPT codes the author supplied (see below)? Unless, you think something is missing?

Vocabulary Code Code Label ICD9CM "V58.44" Aftercare following organ transplant ICD9CM "V42.81" Bone marrow replaced by transplant ICD9CM "996.89" Complications of other specified transplanted organ ICD9CM "996.85" Complications of transplanted bone marrow ICD9CM "996.83" Complications of transplanted heart ICD9CM "996.87" Complications of transplanted intestine ICD9CM "996.81" Complications of transplanted kidney ICD9CM "996.82" Complications of transplanted liver ICD9CM "996.84" Complications of transplanted lung ICD9CM "996.8" Complications of transplanted organ ICD9CM "996.80" Complications of transplanted organ, unspecified ICD9CM "996.86" Complications of transplanted pancreas ICD9CM "V42.1" Heart replaced by transplant ICD9CM "V42.0" Kidney replaced by transplant ICD9CM "V42.7" Liver replaced by transplant ICD9CM "V42.6" Lung replaced by transplant ICD9CM "V42" Organ or tissue replaced by transplant ICD9CM "V42.84" Organ or tissue replaced by transplant, intestines ICD9CM "V42.8" Other specified organ or tissue replaced by transplant ICD9CM "V42.89" Other specified organ or tissue replaced by transplant ICD9CM "V42.83" Pancreas replaced by transplant ICD9CM "V42.82" Peripheral stem cells replaced by transplant ICD9CM "V42.9" Unspecified organ or tissue replaced by transplant CPT4 "S2103" adrenal tissue transplant CPT4 "580" anesthesia for heart transplant or heart/lung transplant CPT4 "38240" bone marrow or blood-derived peripheral stem cell transplantation; CPT4 "38241" bone marrow or blood-derived peripheral stem cell transplantation; CPT4 "38242" bone marrow or blood-derived peripheral stem cell transplantation; CPT4 "0085t" breath test for heart transplant rejection CPT4 "33945p" heart transplant, w/wo re CPT4 "33945" heart transplant, with or without recipient cardiectomy CPT4 "33635-50" heart-lung transplant w/ CPT4 "33935" heart-lung transplant with recipient cardiectomy-pneumonectomy CPT4 "44135" intestinal allotransplantation; from cadaver donor CPT4 "44136" intestinal allotransplantation; from living donor CPT4 "47136" liver allotransplantation; heterotopic, partial or whole, from cadaver CPT4 "47135" liver allotransplantation; orthotopic, partial or whole, from cadaver or CPT4 "S2060" lobar lung transplantatio CPT4 "32854" lung transplant, double (bilateral sequential or en bloc); with CPT4 "32853" lung transplant, double (bilateral sequential or en bloc); without CPT4 "32851p" lung transplant, single CPT4 "32852p" lung transplant, single CPT4 "32852" lung transplant, single; with cardiopulmonary bypass CPT4 "32851" lung transplant, single; without cardiopulmonary bypass CPT4 "48160" pancreatectomy, total or subtotal, with autologous transplantation of CPT4 "44137" removal of transplanted intestinal allograft, complete CPT4 "48556" removal of transplanted pancreatic allograft CPT4 "50370" removal of transplanted renal allograft CPT4 "50365" renal allotransplantation, implantation of graft; with recipient CPT4 "50360" renal allotransplantation, implantation of graft; without recipient CPT4 "50380" renal autotransplantation, reimplantation of kidney CPT4 "S2054" transplantation multivisc CPT4 "48554" transplantation of pancreatic allograft CPT4 "76776" ultrasound, transplanted kidney, real time and duplex doppler with image I believe #2 https://github.com/callahantiff/PheKnowVec/issues/2 is misspelled. Dissecans vs dessicans.

OK, I was legitimately worried that the typo was my fault. Turns, out that "dessicans" is how the phenotype author spelled it and I just copied the spelling mistake. Sort of ironic that even word tried to highlight the typo! 😃 https://user-images.githubusercontent.com/8030363/58522458-b63f2f00-817d-11e9-9e7d-348e1fed9907.png I will run again with the correct spelling and see if we get anything else.

3 https://github.com/callahantiff/PheKnowVec/issues/3, is the 3rd in reference to which version of the test was used? If so, just going with HIV seems appropriate.

Fair question, unfortunately, the only information I am given is this: https://user-images.githubusercontent.com/8030363/58522635-7c225d00-817e-11e9-8aef-2e734ee80c91.png Earlier this year, it was suggested that we focus on the labs listed in a specific CDC Resource https://github.com/callahantiff/PheKnowVec/issues/12#issuecomment-475649701 and here https://github.com/callahantiff/PheKnowVec/issues/12#issuecomment-476486642 you can see what I found form digging it through it and querying our data sources. What are your thoughts?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/callahantiff/PheKnowVec/issues/12?email_source=notifications&email_token=AB3BHS4MESJXWGU7H7KCZALPXXL5ZA5CNFSM4G5OMSIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWN4T7Q#issuecomment-496749054, or mute the thread https://github.com/notifications/unsubscribe-auth/AB3BHS2PCICXX6RQ2QU2ACLPXXL5ZANCNFSM4G5OMSIA.

tdbennett commented 5 years ago

Try small bowel transplant as well

On May 28, 2019, at 9:17 PM, Tiffany J. Callahan notifications@github.com wrote:

@jwyrwa https://github.com/jwyrwa, I missed one sorry! Any alternative strategies for searching "bowel transplant"? I was thinking I could try "intestine transplant" and "intestinal transplant"?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/callahantiff/PheKnowVec/issues/12?email_source=notifications&email_token=AB3BHS7WJILQAL3WS5WCHS3PXXYUZA5CNFSM4G5OMSIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWOBGMQ#issuecomment-496767794, or mute the thread https://github.com/notifications/unsubscribe-auth/AB3BHS4OGFJ6CV3BUWCELOTPXXYUZANCNFSM4G5OMSIA.

jwyrwa commented 5 years ago

I like the HSCT idea, though that term includes sources other than the bone marrow, such as peripheral blood and umbilical cord blood. If there's a way to specify the source, then HSCT could work. Otherwise, I would say that those codes that you listed should have us covered.

For "HIV3rd", it looks like it is referring to the third generation of the immunoassay, which is outdated with regards to clinical guidelines. It looks like LOINC only refers to 4th generation. What about "HIV4th" or just "HIV"?

As for bowel transplant, yes, "intestine" / "intestinal" could work. Other alternatives I can think of are specifying which part of the bowel/intestine, divided into small and large, and subdivided into duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, rectum, anus. The ascending colon, transverse colon, and descending colon can also all be lumped together as "colon" as well.

callahantiff commented 5 years ago

@jwyrwa and @tdbennett - thanks for these great suggestions!

I like the HSCT idea, though that term includes sources other than the bone marrow, such as peripheral blood and umbilical cord blood. If there's a way to specify the source, then HSCT could work. Otherwise, I would say that those codes that you listed should have us covered.

OK, for simplicity I will hold off on adding anything else for this term at this point.

For "HIV3rd", it looks like it is referring to the third generation of the immunoassay, which is outdated with regards to clinical guidelines. It looks like LOINC only refers to 4th generation. What about "HIV4th" or just "HIV"?

We already have "HIV", so I will just add "HIV4th" to the list.

As for bowel transplant, yes, "intestine" / "intestinal" could work. Other alternatives I can think of are specifying which part of the bowel/intestine, divided into small and large, and subdivided into duodenum, jejunum, ileum, cecum, ascending colon, transverse colon, descending colon, rectum, anus. The ascending colon, transverse colon, and descending colon can also all be lumped together as "colon" as well.

Groovy, I will add all of these terms as well as "small bowel transplant" mentioned by @tdbennett and see what we get.

callahantiff commented 5 years ago

Closing this issue as we have resolved all questions at this.

callahantiff / PheKnowVec

TODO - Manuscript Task: Verify Steroid-Induced Osteonecrosis Phenotype #12

3, is the 3rd in reference to which version of the test was used? If so, just going with HIV seems appropriate.

3, is the 3rd in reference to which version of the test was used? If so, just going with HIV seems appropriate.

3 https://github.com/callahantiff/PheKnowVec/issues/3, is the 3rd in reference to which version of the test was used? If so, just going with HIV seems appropriate.