MEDICAL CODING - Clinical trials

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  MedDRA 13.1 MedDRA 13.0 MedDRA 12.1 MedDRA 12.0
LLT 68661 68258 67503 66135
PT 18919 18786 18641 18075
HLT 1709 1709 1699 1688
HLGT 335 335 333 332
SOC 26 26 26 26

Medical coding : (or Term Harmonization) Different Trial Sites, Different culture and Time-zones, Different investigators(physicians) and various other factors leads to variations in the Research Data entered in particular fields. Few of these data like Adverse event and Disease History is essentially entered as free text and thus coding is an essential method to harmonize all these data so that it is analysed properly. The data entered is compared and matched with standard libraries or dictionaries and updated with a data which is uniform and acceptable. Coding may be done automatically (Computer Aided) , manually or a combination of both.

This medical coding is different : If you search for "medical coding" on web , you will be driven to websites which deals with the ICD or CPT medical coding which is different from the coding in clinical trials. The ICD (9,10 etc.) medical coding deals with mapping various medical diagnosis and procedures to codes. This mostly deals with medical insurance data and medical billing. The ICD or CPT coding is out of scope here in this tutorial.

Dictionaries are essential for medical coding. These medical dictionaries contains standardized database with which the  verbatim terms entered in the CRF's is matched. Few Clinical research organizations even keep their own customized dictionary e.g. Drug dictionary .

Various Medical Dictionaries / Thesaurus :

Dictionary / Thesaurus name    Full name        Primary Use
WHOART World Health Organization Adverse Reaction Terminology Adverse event (AE)  coding
COSTART (FDA’s) Coding Symbols for a Thesaurus of Adverse Reaction Terms Adverse event (AE) coding
MedDRA Medical Dictionary for Regulatory Activities Terminology AE / Med. History / Terms coding
ICD (9, 10, 10 CM etc.) International Classification of Diseases (9th / 10th Revision / 10th revision - Clinical Modification) Medical diagnosis and procedures coding
WHODD World Health Organization Drug Dictionary (B1, B2, C) Medication coding (concomitant)

These Dictionaries follow a hierarchal structure for coding. Medical Dictionaries are updated and comes with a newer version periodically.

In what form is it available ? : Consider the case of MedDRA where Dictionary is supplied as bunch of flat ASCII files ($ character separated) with proper documentation and defined data types, so that any standard database system can easily import the file e.g. Create a Oracle template (DBT) using the MedDRA documentation and import the dictionary.
                          MedDRA browser is available as a download from MSSO Website, for those who need to do manual coding. The MedRA ASCII files can be imported to the local computer and used for coding. Automatic coding systems however requires these ASCII data files to be imported to some RDBMS like Oracle, MySQL, PostGRE SQL or as SAS Datasets.

Example > MedDRA table structure SQL >>>

WHO-DD is similarly distributed as ASCII files as well but unlike the MedDRA ascii, the data is organised in fixed positions and is not character separated e.g. in a data row, the characters between 10 to 20 may always contain the Drug name and next characters from 20 to 25 may hold the identifiers of the drug. WHODD browser is also available and it comes with a fat price tag.

Automatic coding (auto-coding) : The complexity of medical terms renders autocoding quite a failure. The "text (verbatim)" terms entered into the system is matched with the terms found in the dictionaries. Autocoders are efficient with "exact" or '100%' matches for the verbatim term and miss-spellings will lead to erroneous or no result. Its not a good idea to rely on autocoding entirely (especially when dealing with medical terms) and the results of Higher level terms sometimes turns out to be funny. Autocoders get confused if two terms are reported simultaneously e.g. fever and rash or fever & rash ; this kind of data entry can't be avoided because clinicians are used to such kind of data recordings.
                          Mostly the autocoders follow fixed and limited algorithms for the medical coding (algorithms are programmed by Software professionals who doesn't care about the essence of Medicine and hence such algorithms turns out to be waste)  . The typical algorithms include text replacements (e.g mild raised temp. and low grade fever is transformed to mild fever) , text removal (e.g. low fever changed to fever), numeral removal (e.g. fever-104 replaced with fever).
                         Another existing problem with most of the autocoding systems is that they tend to apply a common algorithm for various dictionaries that is used for coding within the system. For example when MedDRA and WHODD is used to code AE's and Drug names respectively, a common algorithm for both the dictionaries will yield erroneous result. Few reasons for errors are listed below:

1. Drug names are not always unique (exact text match fails). In fact more than 12,000 drug names are non unique !
2. Same drug may have multiple ATC codes.
3. Similar named drug from the same company may have different ingredients in different countires.
4. Similar named drug from the same company may have different dose strengths in different countires.
5. Similar sounding Drugs may entirely be different.

  A combination of auto and manual coding always works for fast and better results.

Medra terms: (details later in this page)
LLT : Lower level terms
HLT : Higher level terms
HLGT : Higher level group term
SCT : Super class term
SOC : System organ class
Example :
Toothache (LLT)
Toothache (PT)
Dental pian and sensation disorders (HLT)
Dental and Gingival conditions (HLGT)
Gastrointerstinal Disorders (SOC)
Example 2:
Back pain (LLT)
Back Pain (PT)
Musculoskeletal and con. tissue signs and symptoms NEC (HLT)
Musculoskeleteal and connective tissue disorders NEC (HLGT)
Musculoskeletal and connective tissue disorders (SOC)

COSTART terms: (details later in this page)
RT :Reported Term
ET :English Term
SBS :Sub-Body System
PBS :Primary Body System

WHODD: WHODD is available in now available in 2 formats - B and C. Previously format. A was available which is now obsolete. C is the current format and is been in place since last 4-5 years; it contains more information than B format. B is still in place as the older set ups find it difficult to migrate to C yet. For coding of the therapeutic use of drugs, Anatomical Therapeutic Chemical classification (ATC) is used. Each drug is assigned at least one ATC code. ATC - Anatomical-Therapeutic Chemical Classification that is the parts and systems of the human body where the drug might have an effect.

WHO Dictionaries :
1. WHODD : WHO Drug Dictionary
2. WHOHD : WHO Herbal Dictionary
3. WHODDE : WHO Drug Dictionary enhanced

ATC codes : The classification categorises substances at five different levels according to the organ or system on which they act and their chemical, pharmacological and therapeutic properties. There are fourteen main groups (1st level), with one pharmacological/therapeutic subgroup (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level represents the chemical substance

Anatomical Therapeutic Chemical groups - first level
A Alimentary tract and metabolism
B Blood and blood forming organs
C Cardiovascular system
D Dermatologicals
G Genito urinary system and sex hormones
H Systemic hormonal preparations, excl. sex hormones and insulins
J Anti-infectives for systemic use
L Antineoplastic and immunomodulating agents
M Musculo-skeletal system
N Nervous system
P Antiparasitic products, insecticides and repellents
R Respiratory system
S Sensory organs
V Various

Example : Roxithromycin

Level Code Content  
4 J01FA MACROLIDES Chemical subgroup
5 J01FA06 ROXITHROMYCIN Chemical substance


      Tutorial by Dr. Chhanda Mandal  
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