.. _2017_cancer_model_cancers: ======= Cancers ======= This is a common document for the cancers that are modelled similarly in GBD. This document currently has information related to the following cancers: - Tracheal, bronchus and lung cancer - Cervical cancer - Stomach Cancer - Kidney cancer - Gallbladder and biliary tract cancer - Esophageal cancer - Pancreatic cancer - Thyroid cancer - Non-hodgkin lymphoma - Multiple myeloma - Other pharynx cancer - Nasopharynx cancer - Lip and oral cavity cancer - Ovarian cancer - Uterine cancer Any of the other cancers that have similar modelling strategy can be added to this list. Disease Overview ---------------- .. todo:: Add individual definitions of each cancer. In particular, find data about global prevalence and disease fatal and non fatal description. GBD 2017 Modeling Strategy -------------------------- Cancers in GBD 2017 +++++++++++++++++++ GBD 2017 uses similar modeling strategies to estimate the prevalence and resulting disability of these categories of cancers [GBD-2017-YLD-Capstone-Appendix-1-Neoplasms]_. Incidence is estimated directly from mortality using mortality to incidence ratios (MIR). Prevalence for all these cancers are estimated for a maximum of ten years. To estimate the disability, total prevalence for each cancer is split into 1. Diagnosis and primary therapy 2. Controlled phase 3. Metastatic phase 4. Terminal phase .. todo:: Add more details about cancer modeling in GBD 2017. Cause Hierarchy ++++++++++++++++ .. image:: cancers_hierarchy.svg The following table helps to identify cause id and associated sequelae ids for each cancer. .. list-table:: Ids of causes and associated sequelae :widths: 10, 5, 10 :header-rows: 1 * - Cancer - Cause Id - Sequelae Ids * - Esophageal cancer - c_411 - s_244, s_245, s_246, s_247 * - Stomach cancer - c_414 - s_248, s_249, s_250, s_251 * - Tracheal, bronchus and lung cancer - c_426 - s_273, s_274, s_275, s_280 * - Cervical cancer - c_432 - s_282, s_283, s_284, s_285 * - Uterine cancer - c_435 - s_286, s_287, s_288, s_289 * - Lip and oral cavity cancer - c_444 - s_301, s_302, s_303, s_304 * - Nasopharynx cancer - c_447 - s_305, s_306, s_307, s_308 * - Other pharynx cancer - c_450 - s_309, s_310, s_311, s_312 * - Gallbladder and biliary tract cancer - c_453 - s_313, s_314, s_315, s_316 * - Pancreatic cancer - c_456 - s_317, s_318, s_319, s_320 * - Ovarian cancer - c_465 - s_329, s_330, s_331, s_332 * - Kidney cancer - c_471 - s_337, s_338, s_339, s_340 * - Thyroid cancer - c_480 - s_350, s_351, s_352, s_353 * - Non-hodgkin lymphoma - c_485 - s_362, s_363, s_364, s_365 * - Multiple myeloma - c_486 - s_366, s_367, s_368, s_369 Restrictions ++++++++++++ The restrictions table describes any restrictions on the effects of this cause (such as being only fatal or only nonfatal), as well as restrictions on the age and sex of simulants to which different aspects of the cause model apply. For some of the cancer causes in this document, the restrictions differ. So, different tables are used to specify restrictions that are different from others. The following table describes restrictions of the following cancers: - Esophageal cancer - Stomach cancer - Tracheal, bronchus and lung cancer - Lip and oral cavity cancer - Other pharynx cancer - Gallbladder and biliary tract cancer - Pancreatic cancer - Multiple myeloma .. list-table:: Restrictions :widths: 15 15 20 :header-rows: 1 * - Restriction Type - Value - Notes * - Male only - False - * - Female only - False - * - YLL only - False - * - YLD only - False - * - YLL age group start - 15 to 19 - GBD age group id 8 * - YLL age group end - 95 plus - GBD age group id 235 * - YLD age group start - 15 to 19 - GBD age group id 8 * - YLD age group end - 95 plus - GBD age group id 235 The following table describes restrictions of the following cancers: - Cervical cancer - Uterine cancer - Ovarian cancer .. list-table:: Restrictions :widths: 15 15 20 :header-rows: 1 * - Restriction Type - Value - Notes * - Male only - False - * - Female only - True - * - YLL only - False - * - YLD only - False - * - YLL age group start - 15 to 19 - GBD age group id 8 * - YLL age group end - 95 plus - GBD age group id 235 * - YLD age group start - 15 to 19 - GBD age group id 8 * - YLD age group end - 95 plus - GBD age group id 235 The following table describes restrictions of the following cancers: - Kidney cancer - Non-hodgkin lymphoma .. list-table:: Restrictions :widths: 15 15 20 :header-rows: 1 * - Restriction Type - Value - Notes * - Male only - False - * - Female only - False - * - YLL only - False - * - YLD only - False - * - YLL age group start - Early Neonatal - GBD age group id 2 * - YLL age group end - 95 plus - GBD age group id 235 * - YLD age group start - 1 to 4 - GBD age group id 5 * - YLD age group end - 95 plus - GBD age group id 235 The following table describes restrictions of **Nasopharynx cancer**: .. list-table:: Restrictions :widths: 15 15 20 :header-rows: 1 * - Restriction Type - Value - Notes * - Male only - False - * - Female only - False - * - YLL only - False - * - YLD only - False - * - YLL age group start - 5 to 9 - GBD age group id 6 * - YLL age group end - 95 plus - GBD age group id 235 * - YLD age group start - 5 to 9 - GBD age group id 6 * - YLD age group end - 95 plus - GBD age group id 235 The following table describes restrictions of **Thyroid cancer**: .. list-table:: Restrictions :widths: 15 15 20 :header-rows: 1 * - Restriction Type - Value - Notes * - Male only - False - * - Female only - False - * - YLL only - False - * - YLD only - False - * - YLL age group start - 10 to 14 - GBD age group id 7 * - YLL age group end - 95 plus - GBD age group id 235 * - YLD age group start - 10 to 14 - GBD age group id 7 * - YLD age group end - 95 plus - GBD age group id 235 Vivarium Modeling Strategy -------------------------- Scope +++++ .. todo:: Add scope. Assumptions and Limitations +++++++++++++++++++++++++++ 1. Within GBD 2017, after diagnosis/ treatment if a patient survives more than 10 years, they are considered cured for calculating disability. For simulation models, this means that if the simulation is run for more than 10 years, then excess mortality rate exists due to cancer after 10 years and the number of deaths increase. But as per GBD 2017, after 10 years, the patients do not have excess mortality rate. So, this model might over estimate deaths in that scenario. .. todo:: Add more assumptions and limitations. Cause Model Diagram +++++++++++++++++++ Within GBD 2017 data, the remission rate is not available which makes it difficult to transition through the states. So, due to data limitations we are simplifying the model. Note: This simpliflication might over estimate the number of deaths. See Model Assumptions and Limitations section for more information. .. image:: cancer_cause_model.svg State and Transition Data Tables ++++++++++++++++++++++++++++++++ .. list-table:: Definitions :widths: 15 20 30 :header-rows: 1 * - State - State Name - Definition * - S - Susceptible - Susceptible to cancer * - I - Infected - Infected with cancer .. list-table:: States Data :widths: 20 25 30 30 :header-rows: 1 * - State - Measure - Value - Notes * - S - prevalence - 1-prevalence_c{cid} - {cid} represents each cancer in the list of cancers modelled in this document * - S - excess mortality rate - 0 - * - S - disabilty weights - 0 - * - I - prevalence - prevalence_c{cid} - * - I - excess mortality rate - :math:`\frac{\text{deaths\_c\{cid\}}}{\text{population} \times \text{prevalence\_c\{cid\}}}` - * - I - disability weights - :math:`\displaystyle{\sum_{s\in \text{sequelae\_c\{cid\}}}} \scriptstyle{\text{disability\_weight}_s \,\times\, \text{prevalence}_s}` - total disability weight over all sequelae corresponding to the cancer * - ALL - cause specific mortality rate - :math:`\frac{\text{deaths\_c\{cid\}}}{\text{population}}` - .. list-table:: Transition Data :widths: 10 10 10 30 30 :header-rows: 1 * - Transition - Source - Sink - Value - Notes * - i - S - I - :math:`\frac{\text{incidence\_rate\_c\{cid\}}}{\text{1 - prevalence\_c\{cid\}}}` - Incidence rate in total population is divided by 1-prevalence_c{cid} to get incidence rate among the susceptible population. .. list-table:: Data Sources :widths: 20 25 25 25 :header-rows: 1 * - Measure - Sources - Description - Notes * - prevalence_c{cid} - como - Prevalence of cause {cancer} - {cancer} represents each cancer in the list of cancers modelled in this document * - deaths_c{cid} - codcorrect - Deaths from {cancer} - * - population - demography - Mid-year population for given country - * - incidence_rate_c{cid} - como - Incidence rate for {cancer} - * - disability_weight_s{`sid`} - YLD appendix - Disability weights associated with each sequelae - * - prevalence_s{`sid`} - como - Prevalence of each sequelae - Validation Criteria +++++++++++++++++++ .. todo:: Describe tests for model validation. References ---------- .. [GBD-2017-YLD-Capstone-Appendix-1-Neoplasms] Supplement to: `GBD 2017 Disease and Injury Incidence and Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet 2018; 392: 1789–858` (pp. 310-317)