CHeCS

CHRONIC HEPATITIS B & C COHORT STUDY

Abstraction Guidelines

July 19, 2010

Table of Contents

General Comments ...... 3

Liver BIOPSY...... 5

EXTERNAL Labs ...... 7

HBV resistance...... 13

pRIMER on Hepatitis Medications...... 15

Hepatitis Treatment history...... 16

hepatitis medication orders...... 19

hcv medciation change details...... 22

GENERAL COMMENTS:

  • There are six types of information to be abstracted, each with a corresponding data entry screen:
  • Liver biopsy reports – amount of fibrosis reported by the pathologist
  1. External lab results – lab tests the patient obtained outside your health system/facility. Need to abstract results that are not available via programmer query to lab results.
  1. HBV resistance test results – lab tests performed by a reference lab which describe which medications a patient’s Hep B virus has developed resistance to.
  1. Hepatitis treatment history – the types of hepatitis medications that a patient has been treated with historically -- in your health system prior to 1/1/06 (or earlier if your electronic orders were complete prior to 1/1/06) or external to your health system, if reported.
  1. Hepatitis medication orders – hepatitis drug orders (outpatient prescriptions) 1/1/06-12/31/08. Abstract only those orders that have not been provided electronically. To our knowledge, Henry Ford is the only site that needs to abstract full orders. However, all sites need to complete “Days Supply per Fill” and “Number of Refills”, if missing, from Hepatitis C drug orders.
  1. HCV medication change detail – occurrences of medication stops, restarts, dosage reductions & dosage increases for HCV drugs only
  • General rules:
  • Vocabulary:
  • HBV=hepatitis B virus
  • HCV=hepatitis C virus
  • hepatitis B patient = hep B patient = HBV patient
  • hepatitis C patient = hep C patient = HCV patient
  1. For date fields:
  2. Enter exact date if documented
  3. Always in MM/DD/YYYY format

 If only the month/year is documented, date=MM/15/YYYY

 If only the year is documented, date=07/01/YYYY

  1. For time fields:
  2. Enter in military time (24 hour clock)
  3. Always in HH:MM format
  • Please note if patient doesn’t seem to belong in the chronic hepatitis B or C cohort
  • If there is no mention of hepatitis ever, or you see any mention that patient is not chronic and/or doesn’t need follow-up for hepatitis
  • Patient’s study ID should be put on a “needs to be verified” list and sent to the Project Coordinator.
  • If a patient is included in the HBV cohort and appears to have Hep C instead, or vice versa
  • Patient’s study ID should be put on a “needs to be verified” list and sent to the Project Coordinator.
  • Project Coordinator should have a clinician review for a determination.
  • For those determined as ineligible for the cohort, the Project Coordinator will initiate a process for removing that patient from the cohort and removing their data from the data set.

 This process will be outlined at a later date

LIVER BIOPSY:

Scope: Abstract from liver biopsy reports as far back as documentation is available in the EMR.
Where to look (within the date ranges detailed below for each site):
Anatomic pathology reports. Unless these biopsy reports are very easy to find in the EMR, it may be best to work from a list of patients known to have had liver biopsies, based on billing codes.
Dates to be abstracted:
Geisinger:
[Earliest available EMR documentation] –thru– 12/31/08 / Henry Ford:
[Earliest available EMR documentation] –thru– 12/31/08 / KP-Hawaii:
[Earliest available EMR documentation] –thru– 12/31/08 / KP-NW:
[Earliest available EMR documentation] –thru– 12/31/08 / Lovelace:
tbd

Abstraction guidelines:

  • “Biopsy date” is the date the biopsy was performed
  • A required field and can not be left blank
  • Year must be ≥ 1980 and ≤ 2015.
  • “Biopsy/Fibrosis Stage”
  • Select the appropriate stage under the scale documented on the biopsy report
  • 6 Scales available

 IASL Scale

 Batts - Ludwig Scale

 Metavir Scale

 Ishak Scale

 Knodell Scale

 Unknown Scale

  1. If your pathologists don’t routinely document the scale they’re using in the report, find out from the Pathology department which scale they use (this may differ at different points in time)
  2. If you don’t know the scale, but a stage is given, report the results under the “Unknown Scale”
  3. The pathologist may list a fibrosis stage using more than one scale. If so, enter all stages given.
  4. When entering the stage, use the text associated with the score on the screen drop-down to see if it matches the description provided by the pathologist (to double check you’re using the right scale.)
  • “No Staging Found” - if no stage is given, check the “no staging found” box
  • Fibrosis Description” - If scale is unknown or no staging is found, look for sentence(s) in the Pathology report that describe the amount/extent of fibrosis. Type those sentence(s) into this box. (up to 150 char).
  • “Pathology Diagnosis” – If scale is unknown or no staging is found, type the full pathologist’s diagnosis into this box. (up to 250 char).

See examples
LABS EXTERNAL FORM:

Scope:
  1. Abstract all CHeCS labs back to 1/1/06 that were performed outside your System and are NOT available via programmer query, but can be “seen” in your EMR.
  2. Abstract all ALT and hepatitis DNA/RNA test results from outside your System that are NOT available via programmer query but can be “seen” in your EMR, as far back as documentation is available in the EMR.
Where to look (within the date ranges detailed below for each site):
  • scanned documents
  • hepatitis-care specialists’ progress/consultation notes (if these test results are likely to be documented/dictated in those notes)
  • hepatitis-care clinic shadow charts, if available.
(Note: These are lab tests for which the patient had their lab work done outside your health system/facility. These results are generally not available via programmer query. At some study sites, patients may not ever go outside the health plan/system to get labwork done while in the health plan, so there may not be very many “external” labs.)
Dates to be abstracted:
Geisinger:
  • For all CHeCS labs except those listed below:
1/1/06 –thru– [12/31/08 or Abstract Date]
  • For ALT and hepatitis DNA/RNA test results only:
[Earliest available EMR documentation] –thru– 12/31/08 / Henry Ford:
  • For all CHeCS labs except those listed below:
1/1/06 –thru– [12/31/08 or Abstract Date]
  • For ALT and hepatitis DNA/RNA test results only:
[Earliest available EMR documentation] –thru– 12/31/08 / KP-Hawaii:
  • For all CHeCS labs except those listed below:
1/1/06 –thru– [12/31/08 or Abstract Date]
  • For ALT and hepatitis DNA/RNA test results only:
[Earliest available EMR documentation] –thru– 12/31/08 / KP-NW:
  • For all CHeCS labs except those listed below:
1/1/06 –thru– [12/31/08 or Abstract Date]
  • For ALT and hepatitis DNA/RNA test results only:
[Earliest available EMR documentation] –thru– 12/31/08 / Lovelace:
tbd

Abstraction guidelines:

  • “Lab Date” and “Lab Time”
  • Can be entered just once and multiple tests can be inserted under the same date and time.
  • Lab Date is the date the lab was collected
  • A required field and can not be left blank
  • Year must be ≥ 1980 or ≤ 2015.
  • Lab Time is the time the lab was collected
  • A required field and can not be left blank
  • If time is unknown, enter “00:00”
  • “Lab Group/Tests”
  • The lab tests drop-down list changes according to the lab group selected.
  1. Below is a list of each lab group and the applicable lab tests to be abstracted; including the expected result type (numeric or non-numeric)
  • Hep A

Short Test Name / Full Test Name / Numeric or Non-Numeric
HAABG / Hep A antibody IGG / Non-Numeric
HAABM / Hep A antibody IGM / Non-Numeric
HAABT / Hep A Total (IGG+IGM) / Non-Numeric
  • Hep B

Short Test Name / Full Test Name / Numeric or Non-Numeric
HBcABG / Hep B core antibody IGM / Non-Numeric
HBcABM / Hep A antibody IGM / Non-Numeric
HBcABT / Hep B core antibody Total (IGG+IGM) / Non-Numeric
HbeAB / Hep B e antibody / Non-Numeric
HbeAG / Hep B e antigen / Non-Numeric
HBsAB / Hep B surface antibody / Non-Numeric
HBsABQT / Hep B surface antibody – quantitative / Numeric
HbsAG / Hep B surface antigen / Non-Numeric
HBVQL / Hep B DNA qual. (qualitative) / Non-Numeric
HBVQT / Hep B DNA quant. (quantitative) / See *EXCEPTIONS*
HBVQTL / Hep B DNA quant. – log value / See *EXCEPTIONS*
  • Hep C

Short Test Name / Full Test Name / Numeric or Non-Numeric
HCAB / Hep C antibody – Elisa / Non-Numeric
HCABG / Hep C antibody – IGG / Non-Numeric
HCABR / Hep C antibody – RIBA / Non-Numeric
HCVG / Hep C RNA genotype / Non-Numeric
HCVQL / Hep C RNA qual. (qualitative) / Non-Numeric
HCVQT / Hep C RNA quant. (quantitative / See *EXCEPTIONS*
HCVQTL / Hep C RNA quant. – log value / See *EXCEPTIONS*
  • Hep D & E

Short Test Name / Full Test Name / Numeric or Non-Numeric
HDAB / Hep D (delta) antibody / Non-Numeric
HEABM / Hep E antibody IGM / Non-Numeric
HEABG / Hep E antibody IGG / Non-Numeric
HEABT / Hep E antibody Total (IGG+IGM) / Non-Numeric
  • HIV

Short Test Name / Full Test Name / Numeric or Non-Numeric
HIVAB / HIV antibody (Elisa) / Non-Numeric
HIVAB_WB / HIB antibody (Western Blot) / Non-Numeric
CD4 / CD4 T-cell count (count, not %) / Numeric
HIVQL / HIV DNA qual. (qualitative) / Non-Numeric
HIVQT / HIV DNA quant. (quantitative) / See *EXCEPTIONS*
  • Liver Profile

Short Test Name / Full Test Name / Numeric or Non-Numeric
ALT / ALT/SGPT / Numeric
AST / AST/SGOT / Numeric
ALBUMIN / Albumin (blood) / Numeric
ALP / Alkaline phosphatase / Numeric
BILI_TOT / Total Bilirubin / Numeric
TOT_PROT / Total Protein / Numeric
  • Biochem Profile

Short Test Name / Full Test Name / Numeric or Non-Numeric
ALT / ALT/SGPT / Numeric
AST / AST/SGOT / Numeric
A_G_Ratio / A/G ratio / Numeric
ALBUMIN / Albumin (blood) / Numeric
ALP / Alkaline phosphatase / Numeric
BILI_TOT / Total Bilirubin / Numeric
TOT_PROT / Total Protein / Numeric
BUN / Blood Urea Nitrogen / Numeric
CREATININE / Creatinine / Numeric
GFR / Glomular Filtration Rate / See *EXCEPTIONS*
GLU_F / Glucose - fasting / Numeric
GLU_RAN / Glucose - random/non-spec / Numeric
  • Lipid Profile

Short Test Name / Full Test Name / Numeric or Non-Numeric
TOT_Choles / Cholesterol Total / Numeric
HDL / HDL / Numeric
LDL_CLC_F / LDL (calc.- fasting) / Numeric
LDL_CLC_NS / LDL (calc.- unknown if fasting) / Numeric
LDL_Direct / LDL (direct) / Numeric
LDL_NS / LDL (method not indicated) / Numeric
TRIG_F / Triglyceride – fasting / Numeric
TRIG_NS / Triglyceride – random/non-spec / Numeric
  • CBC / Coag / Hematology

Short Test Name / Full Test Name / Numeric or Non-Numeric
ANC / Absolute Neutrophil Count / Numeric
HCT / Hematocrit / Numeric
HGG / Hemoglobin / Numeric
PLT / Platelet Count / Numeric
WBC / White Blood Count / Numeric
INR / International Normalized Ratio / Numeric
PT / Prothrombin Time / Numeric
  • Thyroid Profile

Short Test Name / Full Test Name / Numeric or Non-Numeric
TSH / Thyroid stimulating hormone / Numeric
U_TSH / Ultra sensitive Thyroid stimulating hormone / Numeric
  • Other

Short Test Name / Full Test Name / Numeric or Non-Numeric
AFP / Alpha feto-protein (blood/serum) (Not amniotic/maternal) / Numeric
CRP / C Reactive Protein / Numeric
CRPHS / High sensitivity C- Reactive Protein / Numeric
GGT / Gamma Glutamyl Transferase / Numeric
HGBA1C / Hemoglobin A1C / Numeric
LDH / Lactic dehydrogenase / Numeric
  1. The following lab tests may be collected under both a Liver Profile and the Biochem Profile Lab group
  2. ALT/SGPT
  3. AST/SGOT
  4. Albumin
  5. ALP – Alkaline phosphatase
  6. BILT – Total Bilirubin
  7. TP – Total Protein
  1. *EXCEPTIONS* are explained at the end of this section
  • “Numeric Results”
  • No special characters allowed
  • < or >
  • Field must be completed for all labs with a quantitative result
  • Field should be left blank for all labs with a qualitative result
  • “Result Unit”
  • Field must be completed for all labs with a numeric result
  • Select the appropriate unit from the drop-down list provided

Page 1 of 24

  • %
  • cells/µL
  • copies/mL
  • g/dL
  • IU/L
  • IU/mL
  • K/cumm
  • k/µL
  • log copies/mL
  • log IU/mL
  • MEQ/L
  • mg/dL
  • mg/L
  • ng/mL
  • mIU/mL
  • mL/min/1.73m2
  • Other
  • pg/mL
  • seconds
  • µIU/mL
  • unitless ratio
  • unknown
  • unlisted

Page 1 of 24

  • “Non-Numeric Results”
  • Field must be completed for all labs with a qualitative result
  • Select the appropriate unit from the drop-down list provided
  • N- Negative
  • P- Positive
  • I- Indeterminate/Borderline
  • R-Reactive
  • NR- Non-Reactive
  • W- Weakly reactive
  • < - Less than LLD *
  • >- Above ULD*
  • NOR- Normal GFR*
  • Genotypes 1,1a, 1b, 1c, 2, 2a, 2b, 2c, 3, 3a, 3b, 4, 4a, 4b, 4c, 4d, 4e, 5, 6; or “Could not be genotyped”

(* - more details below)

  1. Field should be left blank for all quantitative results
  2. Field is set to 9999(Null) by default
  • “LLN/LLD” and “ULN/ULD”
  1. For “LLN/LLD”, enter the Lower Limit Normal or Lower Limit of Detection as applicable to the lab test
  1. For “ULN/ULD”, enter the Upper Limit Normal or Upper Limit of Detection as applicable to the lab test.
  1. Normals are generally reported for quantitative tests, and are most frequently given as a range (“reference range”). You should enter the lower end of the reference/normal range as “LLN/LLD”, and the upper end as “ULN/ULD”.

 Some normals are not reported as a range. Examples:

  • If the normal is listed as “>50”, then anything above 50 is considered a normal value. Thus 50 is the lower limit of normal and you should enter 50 for “LLN/LLD”
  • If the normal is listed as “<14.5”, then anything below 14.5 is considered a normal value. Thus 14.5 is the upper limit of normal and you should enter 14.5 for “ULN/ULD”
  1. Most tests with results reported as “positive/negative/indeterminate” (qualitative tests) will not have an LLN/LLD.
  2. Exceptions include: HBVQL, HCVQL, HIVQL

 For these tests you will usually see a lower limit of detection listed (ex. < 200). In is example, 200 is the lower limit of detection and you would enter 200 as the “LLN/LLD”

 For these test you will sometimes though rarely see an upper limit of detection listed (ex. > 1 million). In these cases enter 1000000 as the ULD

Page 1 of 24

  • “Abnormal Indicator”
  • Field is set to ‘Unknown’ by default
  • Select the appropriate indicator from the drop-down list provided
  • Normal
  • Abnormal
  • Unknown
  • You should almost always be able to choose normal or abnormal
  • *EXCEPTIONS* - Tests
  1. GFR
  2. If a numeric result is provided in the test report

 Enter that value in the “Numeric Result” field

  • If the result is given as >60 (example) and inclusive in the normal range

 Choose “NOR – Normal GFR” in the “Non-Numeric Result” field

  • In all instances enter the LLN and ULN as provided in the normal range of the test report
  • Always select the appropriate “Abnormal Indicator”
  1. Viral Load Tests ( HBVQT, HBVQTL, HCVQT, HCVQTL, & HIVQT)
  2. If a numeric result is provided in the test report

 Enter that value in the “Numeric Result” field

  • If the result is given as “<43” (example), this is a normal test result and the LLD is 43

 Choose “< - Less than LLD” in the “Non-Numeric Result” field

 Enter 43 in the “LLN/LLD” field

 “Abnormal Indicator” = Normal

  • If the result is given as “>1,000,000” (example), this is a viral load above the limit of detection and is an abnormal result.

 Choose >- Above ULD” in the “Non-Numeric Result” field

 Enter 1000000 in the “ULN/ULD” field

 “Abnormal Indicator” = Abnormal See examples

HBV RESISTANCE:

Scope: Abstract HBV resistance test results as far back as documentation is available in the EMR. (These tests are not performed on very many patients, but the results are very important.)
Where to look (within the date ranges detailed below for each site):
It may be best to generate a list of the patients that had HBV resistance tests and when, based on billing codes, so the abstractor knows to look for a resistance test report.
  • scanned documents
  • hepatitis-care specialists’ progress / consultation notes (if these test results are likely to be documented/dictated in those notes)
  • hepatitis-care clinic shadow charts, if available.
Dates to be abstracted:
Geisinger:
[Earliest available EMR documentation] –thru– 12/31/08 / Henry Ford:
[Earliest available EMR documentation] –thru– 12/31/08 / KP-Hawaii:
[Earliest available EMR documentation] –thru– 12/31/08 / KP-NW:
[Earliest available EMR documentation] –thru– 12/31/08 / Lovelace:
tbd

Abstraction guidelines:

  • “Collection date” is the date the lab was collected
  1. A required field and can not be left blank
  2. Year must be ≥ 1980 and ≤ 2015.
  • “Collection time” is the time the lab was collected
  • “Antiviral Drugs”
  • Provide the results of the resistance testing for each of the required antiviral drugs
  • Lamivudine (Epivir)
  • Telbivudine (Tyzeka)
  • Famicolvir (Famvir)
  • Adovovir (Hepsera)
  • Entecavir (Baraclude)
  • Valid responses for each antiviral:
  • Yes – Resistant
  • No – Not Resistant
  • Sensitive
  • Not Sensitive
  • “Comments”- enter any comments necessary to explain the results of the particular resistance testing

See examples

PRIMER on HEPATITIS MEDICATIONS:

Hepatitis C meds:

  • Interferons & pegylated interferons
  1. Standard interferons (usually injected 3x/week):
  2. Interferon alfa 2a (sometimes spelled “alpha 2a”) a.k.a. “interferon a”  Brand name=Roferon or Roferon A
  3. Interferon alfa 2b (sometimes spelled “alpha 2b”) a.k.a. “recombinant interferon” or “interferon b”  Brand name=Intron or Intron A
  4. Interferon alfacon-1 (a.k.a. “consensus interferon”)  Brand name=Infergen

Hepatitis is not treated with beta or gamma interferons

  1. Pegylated interferons (“peginterferons”)

Pegylated interferons are newer formulations of interferon that are longer acting and thus need to be injected only 1x/week. They are often more effective and should be distinguished from standard interferons when abstracting, if possible.