# Phenotype Processing Algorithm

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1 Phenotype Processing Algorithm 1. Each individual has three associated variables which will be used for diagnostic classification. The variables are SZ, SA, and BS, which correspond to affection status for Schizophrenia, Schizoaffective Disorder, and Broad Spectrum. Each variable can have the value 0 (phenotype unknown for that diagnosis), 1 (not affected with that diagnosis), or 2 (affected with that diagnosis). 2. Initialize all three variables = 1 3. If person has any code in the SZ_CODES set, set SZ = 2 4. If person has any code in the SA_CODES set, set SA = 2 5. If person has any code in the BS_CODES set, set BS = 2 6. If person has no codes, set SZ=SA=BS = 0; done with this person 7. If person has any code in the GLOBAL_EXCLUDE set, set SZ=SA=BS=0; done with this person 8. If SZ=SA=BS=1: a. If person has any code in the UNAFF_EXCLUDE set, set SZ=SA=BS=0 b. Done with this person 9. If SZ=2: a. If person has any code in the SZ_EXCLUDE set, set SZ=0 b. If person has any code in the SZ_DEMOTE1 set, set SZ=0 and SA=2 c. If person has any code in the SZ_DEMOTE2 set, set SZ=0, SA=0, and BS=2 10. If SA=2: a. If person has any code in the SA_EXCLUDE set, set SA=0 b. If person has any code in the SA_DEMOTE set, set SA=0 and BS=2 11. If BS=2: a. If person has any code in the BS_EXCLUDE set, set BS=0 12. If SZ=2 AND SA=2, set SZ=0 Possible end states: SZ SA BS Classification Diagnosis Affection 2 [0,1] [0,1,2] Schizophrenia 4 Affected [0,1] 2 [0,1,2] Schizoaffective 3 Affected [0,1] [0,1] 2 Broad Spectrum 2 Unknown Unaffected 1 Unaffected Unknown 0 Unknown

2 DSMIIIR [SZ_CODES] Schizophrenia, disorganized type, unspecified Schizophrenia, disorganized type, chronic Schizophrenia, catatonic type, chronic Schizophrenia, paranoid type, unspecified Schizophrenia, paranoid type, chronic Schizophrenia, residual type, unspecified Schizophrenia, residual type, chronic Schizophrenia, undifferentiated type, unspecified Schizophrenia, undifferentiated type, chronic Schizophrenia, paranoid type, chronic with acute exacerbation Schizophrenia, paranoid type, in remission [SA_CODES] Schizoaffective disorder D Schizoaffective disorder, depression type M Schizoaffective disorder, manic type [BS_CODES] Schizophreniform disorder Delusional disorder Psychotic disorder NOS Paranoid personality disorder Schizoid personality disorder Schizotypal personality disorder [GLOBAL_EXCLUDE] 60 Dx Unknown 61 Un Dx Psychosis 62 Un Dx Psychosis, w/ hospitalization 63 Un Dx Psychiatric Disorder w/o hospitalization Presenile dementia NOS OR Primary degenerative dementia of the Alzheimer type, presenile onset, uncomplicated Multi-infarct dementia, uncomplicated Dementia associated with alcoholism Other or unspecified psychoactive substance hallucinosis Delirium (etiology noted on Axis III or is unknown) Organic delusional disorder (etiology noted on Axis III or is unknown) Organic hallucinosis (etiology noted on Axis III or is unknown) Organic mood disorder (etiology noted on Axis III or is unknown)

3 Dementia (etiology noted on Axis III or is unknown) Major depression, single episode, unspecified Major depression, single episode, with psychotic features Major depression, recurrent, unspecified Major depression, recurrent, with psychotic features Bipolar disorder, manic, unspecified Bipolar disorder, manic, with psychotic features Bipolar disorder, mixed, unspecified Bipolar disorder, mixed, with psychotic features Pervasive developmental disorder NOS Unspecified mental disorder (nonpsychotic) Opioid dependence Sedative, hypnotic, or anxiolytic dependence Cocaine dependence Amphetamine or similarly acting sympathomimetic dependence Hallucinogen dependence OR Phencyclidine (PCP) or similarly acting arylcyclohexylamine dependence Inhalant dependence Polysubstance dependence OR Psychoactive substance dependence NOS Hallucinogen abuse OR Hallucinogen hallucinosis Sedative, hypnotic, or anxiolytic abuse OR Sedative, hypnotic, or anxiolytic intoxication Opioid abuse OR Opioid intoxication Cocaine abuse OR Cocaine intoxication Amphetamine or similarly acting sympathomimetic abuse OR Amphetamine or similarly acting sympathomimetic intoxication Organic personality disorder (etiology noted on Axis III or is unknown) Mild mental retardation Moderate mental retardation Unspecified mental retardation Any other diagnosis A Senile dementia NOS B Primary degenerative dementia of the Alzheimer type, senile onset, uncomplicated F Amphetamine or similarly acting sympathomimetic withdrawal C Other or unspecified psychoactive substance delusional disorder D Hallucinogen delusional disorder A Hallucinogen mood disorder B Other or unspecified psychoactive substance mood disorder A Organic mental disorder NOS (etiology noted on Axis III or is unknown) C Major depression, single episode, with psychotic features, mood congruent I Major depression, single episode, with psychotic features, mood incongruent C Major depression, recurrent, with psychotic features, mood congruent I Major depression, recurrent, with psychotic features, mood incongruent C Bipolar disorder, manic, with psychotic features, mood congruent I Bipolar disorder, manic, with psychotic features, mood incongruent A Hallucinogen dependence B Phencyclidine (PCP) or similarly acting arylcyclohexylamine dependence

4 304.90A Polysubstance dependence B Psychoactive substance dependence NOS A Hallucinogen hallucinosis B Hallucinogen Abuse/Dep A Sedative, hypnotic, or axiolytic abuse A Opiod abuse B Opioid intoxication A Cocaine abuse B Amphetamine or similarly acting sympathomimetic abuse A Phencyclidine (PCP) or similarly acting arlycyclohexylamine abuse C Inhalant abuse D Psychoactive substance abuse NOS E Other or unspecified psychoactive substance intoxication G Inhalant intoxication A Development disorder NOS B Diagnosis or condition deferred on Axis I V40.00 Borderline intellectual functioning [UNAFF_EXCLUDE] Bipolar II Disorder Mood Disorder NOS Personality disorder NOS Depressive disorder NOS A Bipolar disorder, NOS A Diagnosis or condition deferred on Axis II [SZ_EXCLUDE] [SZ_DEMOTE1] Major depression, recurrent, mild Major depression, recurrent, moderate Major depression, recurrent, severe, without psychotic features Major depression, recurrent, in partial remission Major depression, recurrent, in full remission Bipolar disorder, depressed, moderate Bipolar disorder, depressed, in partial remission Bipolar II Disorder Mood Disorder NOS Depressive disorder NOS A Bipolar disorder, NOS

5 [SZ_DEMOTE2] [SA_EXCLUDE] [SA_DEMOTE] [BS_EXCLUDE]

6 DSMIV [SZ_CODES] Schizophrenia, unspecified Schizophrenia, Disorganized Type Schizophrenia, Catatonic Type Schizophrenia, Paranoid Type Schizophrenia, Residual Type Schizophrenia, Undifferentiated Type Schizophrenia, undifferentiated type, chronic [SA_CODES] Schizoaffective Disorder D Schizoaffective disorder, depressive type M Schizoaffective disorder, bipolar type [BS_CODES] Schizophreniform Disorder Brief Psychotic Disorder Psychotic Disorder NOS Paranoid Personality Disorder Schizoid Personality Disorder Schizotypal Personality Disorder /298 Delusional Disorder/Pychotic Disorder Delusional Disorder [GLOBAL_EXCLUDE] Dementia of the Alzheimer's Type, With Late Onset, Uncomplicated (DSMIV) Alcohol-Induced Persisting Dementia Alcohol-Induced Psychotic Disorder, With Hallucinations Alcohol-Induced Psychotic Disorder, With Delusions Alcohol-Related Disorder NOS Amphetamine-Induced Psychotic Disorder, With Delusions OR Cannabis-Induced Psychotic Disorder, With Delusions OR Cocaine-Induced Psychotic Disorder, With Delusions OR Hallucinogen-Induced Psychotic Disorder, With Delusions OR Inhalant-Induced Psychotic Disorder, With Delusions OR Opioid-Induced Psychotic Disorder, With Delusions OR Other (or Unknown) Substance-Induced Psychotic Disorder, With Delusions OR Phencyclidine-Induced Psychotic Disorder, With Delusions OR Sedative-, Hypnotic-, or Anxiolytic-Induced Psychotic Disorder, With Delusions Amphetamine-Induced Anxiety Disorder OR Amphetamine-Induced Sexual Dysfunction OR Amphetamine-Induced Sleep Disorder OR Amphetamine Intoxication OR Caffeine-Induced Anxiety Disorder OR Caffeine-Induced Sleep Disorder OR Cannabis-Induced Anxiety Disorder OR Cannabis Intoxication OR Cocaine-Induced Anxiety Disorder OR Cocaine-Induced Sexual Dysfunction OR Cocaine-Induced Sleep Disorder OR Cocaine

7 Intoxication OR Hallucinogen-Induced Anxiety Disorder OR Hallucinogen Intoxication OR Hallucinogen Persisting Perception Disorder OR Inhalant-Induced Anxiety Disorder OR Inhalant Intoxication OR Opioid-Induced Sexual Dysfunction OR Opioid-Induced Sleep Disorder OR Opioid Intoxication OR Other (or Unknown) Substance-Induced Anxiety Disorder OR Other (or Unknown) Substance-Induced Sexual Dysfunction OR Other (or Unknown) Substance-Induced Sleep Disorder OR Other (or Unknown) Substance Intoxication OR Phencyclidine-Induced Anxiety Disorder OR Phencyclidine Intoxication OR Sedative-, Hypnotic-, or Anxiolytic-Induced Anxiety Disorder OR Sedative-, Hypnotic-, or Anxiolytic-Induced Sexual Dysfunction OR Sedative-, Hypnotic-, or Anxiolytic-Induced Sleep Disorder OR Sedative, Hypnotic, or Anxiolytic Intoxication Psychotic Disorder Due to... [Indicate the General Medical Condition], With Delusions Psychotic Disorder Due to... [Indicate the General Medical Condition], With Hallucinations Mood Disorder Due to... [Indicate the General Medical Condition] Mental Disorder NOS Due to... [Indicate the General Medical Condition] Dementia Due to... [Indicate the General Medical Condition] (DSMIV) Amnestic Disorder NOS OR Dementia NOS Bipolar I Disorder, Single Manic Episode, Unspecified Bipolar I Disorder, Single Manic Episode, Severe With Psychotic Features Major Depressive Disorder, Single Episode, Unspecified Major Depressive Disorder, Single Episode, Severe With Psychotic Features Major Depressive Disorder, Recurrent, Unspecified Major Depressive Disorder, Recurrent, Severe With Psychotic Features Bipolar I Disorder, Most Recent Episode Manic, Severe With Psychotic Features Bipolar I Disorder, Most Recent Episode Depressed, Severe With Psychotic Features Bipolar I Disorder, Most Recent Episode Mixed, Unspecified Bipolar I Disorder, Most Recent Episode Mixed, Severe With Psychotic Features Bipolar I Disorder, Most Recent Episode Unspecified Unspecified Mental Disorder (nonpsychotic) Opioid Dependence Sedative, Hypnotic, or Anxiolytic Dependence Cocaine Dependence Amphetamine Dependence Hallucinogen Dependence Inhalant Dependence (DSMIV) OR Inhalant Dependence OR Phencyclidine Dependence (DSMIVTR) Polysubstance Dependence Hallucinogen Abuse Sedative, Hypnotic, or Anxiolytic Abuse Opioid Abuse Cocaine Abuse Amphetamine Abuse Caffeine Intoxication OR Inhalant Abuse OR Other (or Unknown) Substance Abuse OR Phencyclidine Abuse Learning Disorder NOS 317 Mild Mental Retardation Moderate Mental Retardation Severe Mental Retardation 319 Mental Retardation, Severity Unspecified Any other diagnosis

8 799.9 Diagnosis Deferred on Axis II OR Diagnosis or Condition Deferred on Axis I A Dementia due to Creutzfeldt-Jakob disease C Dementia of the Alzheimer's type, with early onset, uncomplicated 291.8B Alcohol-induced mood disorder A Amphetamine-induced psychotic disorder, with delusions G Other (or unknown) substance-induced psychotic disorder, with delusions A Amphetamine-induced psychotic disorder, with hallucinations B "Cannabis-induced psychotic disorder, with hallucinations" C Cocaine-induced psychotic disorder, with hallucinations G Other (or unknown) substance-induced psychotic disorder, with hallucinations B Cocaine-induced mood disorder F Other (or unknown) substance-induced mood disorder 292.9I Other (or unknown) substance-related disorder NOS B Catatonic disorder due to [Indicate the general medical condition] 294.8B Dementia NOS 294.9A Cognitive disorder NOS 294.9B Dementia due to HIV disease C Major Depressive Disorder, Recurrent, Severe With Psychotic Features, Mood Congruent I Major Depressive Disorder, Recurrent, Severe With Psychotic Features, Mood Incongruent A Bipolar I disorder, most recent episode hypomanic B Bipolar I disorder, most recent episode manic, unspecified C Bipolar I Disorder, Most Recent Episode Unspecified, Severe With Psychotic Features, Mood Congruent I Bipolar I Disorder, Most Recent Episode Unspecified, Severe With Psychotic Features, Mood Incongruent B Pervasive developmental disorder NOS A Other (or unknown) substance dependence B Phencyclidine dependence 304.xx/305 Other (or Unknown) Substance Dependence/Alcohol Abuse B Inhalant abuse C Other (or unknown) substance abuse D Phencyclidine abuse 799.9B Diagnosis or condition deferred on Axis I V62.89 Borderline Intellectual Functioning OR Phase of Life Problem OR Religious or Spiritual Problem V62.89A Borderline intellectual functioning [UNAFF_EXCLUDE] Bipolar Disorder NOS Bipolar II Disorder Mood Disorder NOS Personality Disorder NOS 311 Depressive Disorder NOS 799.9A Diagnosis deferred on Axis II

9 [SZ_EXCLUDE] [SZ_DEMOTE1] Bipolar I Disorder, Single Manic Episode, Moderate Major Depressive Disorder, Recurrent, Mild Major Depressive Disorder, Recurrent, Moderate Major Depressive Disorder, Recurrent, Severe Without Psychotic Features Major Depressive Disorder, Recurrent, In Partial Remission Major Depressive Disorder, Recurrent, In Full Remission Bipolar I Disorder, Most Recent Episode Manic, Mild Most Recent Episode Manic, In Full Remission Bipolar I Disorder, Most Recent Episode Depressed, Moderate Bipolar I Disorder, Most Recent Episode Depressed, In Partial Remission Bipolar I Disorder, Most Recent Episode Depressed, In Full Remission Bipolar Disorder NOS Bipolar II Disorder Mood Disorder NOS 311 Depressive Disorder NOS [SZ_DEMOTE2] [SA_EXCLUDE] [SA_DEMOTE] [BS_EXCLUDE]

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