翻译 - TCGAbiolinks 4 - Clinical data
TCGAbiolinks：临床数据
发表时间：2019年3月20日
TCGAbiolinks提供了一些搜索，下载和解析临床数据的函数。本节首先解释GDC中临床信息的不同来源，然后提供访问不同来源临床数据的必要函数，最后显示不同来源临床数据之间的不一致。
1. 一些有用的信息
1.1. 临床数据：不同来源
在GDC数据库中，可以从两个来源检索临床数据：
- Clinical indexed：使用XML文件创建的精炼的临床数据。
- XML：完成的临床信息文件
1.2. 临床数据：不同来源数据的区别：
- XML文件有更多的信息：辐射，药物信息，后续，生物样本等。而Clinical indexed只是XML文件的一个子集
- Clinical indexed包含更新后的数据，这个数据包含后续信息。例如：如果患者在第一次收集临床数据时仍然存活，并且在下一次随访中死亡，则：1）Clinical indexed将显示为死亡；2）而XML将有两个字段，一个是第一个时间段显示他还活着（在临床部分），另一个字段显示在后续中他死亡。你可以在这里看到这种情况：
2. Clinical indexed：数据获取
在这个例子中，我们将获取Clinical indexed数据。
clinical <- GDCquery_clinic(project = "TCGA-LUAD", type = "clinical")
datatable(clinical, filter = 'top',
options = list(scrollX = TRUE, keys = TRUE, pageLength = 5),
rownames = FALSE)
| submitter_id | classification_of_tumor | last_known_disease_status | updated_datetime | primary_diagnosis | tumor_stage | age_at_diagnosis | vital_status | morphology | days_to_death | days_to_last_known_disease_status | created_datetime | state | days_to_recurrence | diagnosis_id | tumor_grade | tissue_or_organ_of_origin | days_to_birth | progression_or_recurrence | prior_malignancy | site_of_resection_or_biopsy | days_to_last_follow_up | cigarettes_per_day | weight | alcohol_history | alcohol_intensity | bmi | years_smoked | exposure_id | height | gender | year_of_birth | race | demographic_id | ethnicity | year_of_death | treatment_id | therapeutic_agents | treatment_intent_type | treatment_or_therapy | bcr_patient_barcode | disease |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TCGA-05-4244 | not reported | not reported | 2018-09-06T21:10:41.393019-05:00 | Adenocarcinoma, NOS | stage iv | 25752 | alive | 8140/3 | released | 71222be8-573b-5d40-a15e-57649e0aec0a | not reported | Lower lobe, lung | -25752 | not reported | not reported | Lower lobe, lung | 0 | 2.08219178082192 | 19e0b9d9-717b-53b1-a0f4-44ca005aeedd | male | 1939 | not reported | 139ab7b9-af85-58e3-ac01-933eeae4afb9 | not reported | 834430fa-3aa8-570c-bac0-0c09865fbb2b | TCGA-05-4244 | LUAD | ||||||||||||||
| TCGA-05-4245 | not reported | not reported | 2018-09-06T21:10:41.393019-05:00 | Adenocarcinoma, NOS | stage iiia | 29647 | alive | 8140/3 | released | e2fb63d6-2eac-535c-bcd0-e9575ebaf006 | not reported | Upper lobe, lung | -29647 | not reported | not reported | Upper lobe, lung | 730 | 1.75342465753425 | 8d858a93-54e3-5432-9589-68c6b90a24c8 | male | 1928 | not reported | 3ec79286-1857-5eeb-a778-0c86ff2a13f6 | not reported | 85506557-5c39-5d73-ba25-228aee1aea2a | TCGA-05-4245 | LUAD |
显示部分结果
3. XML：临床数据解析
直接从XML获取临床数据的过程如下：
- 使用
GDCquery和GDCDownload函数搜索/下载生物样本（biospecimen）或临床XML文件 - 使用
GDCprepare_clinic函数解析XML文件。
需要注意的是，一名患者与其他临床信息之间的关系为：1:n，即一名患者可以有多个相同的临床信息，比如一名患者可以进行多次放射治疗。出于这个原因，在解析XML的时候，TCGAbiolinks只提供某个临床信息的单个表，比如只有药物信息、或者只有辐射通知等。通过clinical.info可以获得对应的临床信息。
3.1. clinical.info参数
对于每一个数据类别，clinical.info可以提供的信息如下：
| data.category | clinical.info |
|---|---|
| Clinical | drug |
| Clinical | admin |
| Clinical | follow_up |
| Clinical | radiation |
| Clinical | patient |
| Clinical | stage_event |
| Clinical | new_tumor_event |
| Biospecimen | sample |
| Biospecimen | bio_patient |
| Biospecimen | analyte |
| Biospecimen | aliquot |
| Biospecimen | protocol |
| Biospecimen | portion |
| Biospecimen | slide |
| Other | msi |
3.2. 数据获取案例
以下是直接从临床XML文件中获取临床数据的几个示例。
-
病人的临床信息：
library(TCGAbiolinks) library(SummarizedExperiment) query <- GDCquery(project = "TCGA-COAD", data.category = "Clinical", file.type = "xml", barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) GDCdownload(query) clinical <- GDCprepare_clinic(query, clinical.info = "patient") datatable(clinical, options = list(scrollX = TRUE, keys = TRUE), rownames = FALSE)bcr_patient_barcode additional_studies tumor_tissue_site histological_type other_dx gender vital_status days_to_birth days_to_last_known_alive days_to_death days_to_last_followup race_list tissue_source_site patient_id bcr_patient_uuid history_of_neoadjuvant_treatment informed_consent_verified icd_o_3_site icd_o_3_histology icd_10 tissue_prospective_collection_indicator tissue_retrospective_collection_indicator days_to_initial_pathologic_diagnosis age_at_initial_pathologic_diagnosis year_of_initial_pathologic_diagnosis person_neoplasm_cancer_status ethnicity weight height day_of_form_completion month_of_form_completion year_of_form_completion residual_tumor anatomic_neoplasm_subdivision primary_lymph_node_presentation_assessment lymph_node_examined_count number_of_lymphnodes_positive_by_he number_of_lymphnodes_positive_by_ihc preoperative_pretreatment_cea_level non_nodal_tumor_deposits circumferential_resection_margin venous_invasion lymphatic_invasion perineural_invasion_present microsatellite_instability number_of_loci_tested number_of_abnormal_loci kras_gene_analysis_performed kras_mutation_found kras_mutation_codon braf_gene_analysis_performed braf_gene_analysis_result synchronous_colon_cancer_present history_of_colon_polyps colon_polyps_present loss_expression_of_mismatch_repair_proteins_by_ihc loss_expression_of_mismatch_repair_proteins_by_ihc_results number_of_first_degree_relatives_with_cancer_diagnosis radiation_therapy postoperative_rx_tx primary_therapy_outcome_success has_new_tumor_events_information has_drugs_information has_radiations_information has_follow_ups_information project stage_event_system_version stage_event_clinical_stage stage_event_pathologic_stage stage_event_tnm_categories stage_event_psa stage_event_gleason_grading stage_event_ann_arbor stage_event_serum_markers stage_event_igcccg_stage stage_event_masaoka_stage TCGA-AA-3972 Colon Colon Adenocarcinoma Yes MALE Alive -26360 0 AA 3972 93cd5d07-e0d3-40f8-ae7f-beadb1efb7c1 No YES C18.7 8140/3 C18.7 NO YES 0 72 2008 WITH TUMOR 18 5 2010 R2 Sigmoid Colon YES 12 3 5.15 NO NO NO NO NO NO NO 0 YES YES NO YES TCGA-COAD 6th Stage IV T3N1M1 TCGA-AA-3972 Colon Colon Adenocarcinoma Yes MALE Alive -26360 0 AA 3972 93cd5d07-e0d3-40f8-ae7f-beadb1efb7c1 No YES C18.7 8140/3 C18.7 NO YES 0 72 2008 WITH TUMOR 18 5 2010 R2 Sigmoid Colon YES 12 3 5.15 NO NO NO NO NO NO NO 0 YES YES NO YES TCGA-COAD 6th Stage IV T3N1M1 TCGA-RU-A8FL Colon Colon Adenocarcinoma No MALE Alive -18975 921 BLACK OR AFRICAN AMERICAN RU A8FL 5F6ED48B-3B5A-4D20-8FBF-C9AA3FEEA186 No YES C18.0 8140/3 C18.0 NO YES 0 51 2011 WITH TUMOR NOT HISPANIC OR LATINO 125 187.96 24 1 2014 R0 Cecum YES 21 5 24.6 NO 65 NO YES NO NO NO NO NO NO 0 NO YES Partial Remission/Response YES YES YES YES TCGA-COAD 7th Stage IIIB T3N2aMX -
药物的临床信息：
clinical.drug <- GDCprepare_clinic(query, clinical.info = "drug") datatable(clinical.drug, options = list(scrollX = TRUE, keys = TRUE), rownames = FALSE)bcr_patient_barcode tx_on_clinical_trial regimen_number bcr_drug_barcode bcr_drug_uuid total_dose total_dose_units prescribed_dose prescribed_dose_units number_cycles days_to_drug_therapy_start days_to_drug_therapy_end therapy_types drug_name clinical_trail_drug_classification regimen_indication regimen_indication_notes route_of_administrations therapy_ongoing measure_of_response day_of_form_completion month_of_form_completion year_of_form_completion project TCGA-AA-3972 NO TCGA-AA-3972-D37426 45D2A60B-C35E-4BAC-9769-B1D5C0153FED 60 1246 Chemotherapy Capecitabine NO Clinical Progressive Disease 3 12 2012 TCGA-COAD TCGA-AA-3972 NO TCGA-AA-3972-D37426 45D2A60B-C35E-4BAC-9769-B1D5C0153FED 60 1246 Chemotherapy Capecitabine NO Clinical Progressive Disease 3 12 2012 TCGA-COAD 只显示了部分信息
-
放射的临床信息：
clinical.radiation <- GDCprepare_clinic(query, clinical.info = "radiation") datatable(clinical.radiation, options = list(scrollX = TRUE, keys = TRUE), rownames = FALSE)bcr_patient_barcode bcr_radiation_barcode bcr_radiation_uuid days_to_radiation_therapy_start days_to_radiation_therapy_end radiation_type radiation_type_notes radiation_dosage units numfractions anatomic_treatment_site regimen_indication regimen_indication_notes radiation_treatment_ongoing course_number measure_of_response day_of_form_completion month_of_form_completion year_of_form_completion project TCGA-RU-A8FL TCGA-RU-A8FL-R68275 07403C45-7D5F-4DAB-AFD2-0AC913DD0AFB 788 788 Internal 568.1 Gy 5 Distant Recurrence NO Stable Disease 14 11 2014 TCGA-COAD -
临床管理的信息：
clinical.admin <- GDCprepare_clinic(query, clinical.info = "admin") datatable(clinical.admin, options = list(scrollX = TRUE, keys = TRUE), rownames = FALSE)bcr_patient_barcode bcr file_uuid batch_number project_code disease_code day_of_dcc_upload month_of_dcc_upload year_of_dcc_upload patient_withdrawal program dbgap_registration_code project TCGA-AA-3972 Nationwide Children's Hospital EA58E3D4-40E0-406F-A7A3-C7C282CFA203 41.78.0 TCGA COAD 22 12 2016 false TCGA-COAD TCGA-AA-3972 Nationwide Children's Hospital EA58E3D4-40E0-406F-A7A3-C7C282CFA203 41.78.0 TCGA COAD 22 12 2016 false TCGA-COAD
3.3. 微卫星标记（Microsatellite）数据
MSI-Mono-Dinucleotide Assay可以测试：1）一组四个单核苷酸重复基因座（ mononucleotide repeat loci），包括polyadenine tracts BAT25、BAT26、BAT40 和 transforming growth factor receptor type II；2）三个二核苷酸重复基因座（dinucleotide repeat loci），包括CA repeats in D2S123、D5S346 和 D17S250。在该测定中包括两个额外的五核苷酸基因座（pentanucleotide loci），包括Penta D和Penta E，可以被用来评估样品特性。如果在肿瘤和匹配的非肿瘤组织或单核血细胞之间检测到微卫星标记数目的变化，则使用多重荧光标记的PCR和毛细管电泳来鉴定MSI。通过singleplex PCR重新评估等同或失败的标记物。
**分类：**1） microsatellite-stable (MSS)；2） low level MSI (MSI-L) ：如果少于40％的标记被改变；3） high level MSI (MSI-H)：如果大于40％的标记被改变。
参考：TCGA维基
Level 3的数据已经包含在提交的BCR临床数据中中，可以按如下方式下载：
library(TCGAbiolinks)
library(SummarizedExperiment)
query <- GDCquery(project = "TCGA-COAD",
data.category = "Other",
legacy = TRUE,
access = "open",
data.type = "Auxiliary test",
barcode = c("TCGA-AD-A5EJ","TCGA-DM-A0X9"))
GDCdownload(query)
msi_results <- GDCprepare_clinic(query, "msi")
datatable(msi_results, options = list(scrollX = TRUE, keys = TRUE))
| bcr_aliquot_uuid | mononucleotide_and_dinucleotide_marker_panel_analysis_status | mononucleotide_marker_panel_analysis_status | bcr_patient_barcode | |
|---|---|---|---|---|
| 1 | 6139cab7-959f-4c49-b9e7-cc25ea8e041c | MSI-H | TCGA-AD-A5EJ | |
| 2 | 511f645e-f107-4f58-9c6a-6f931e612bd6 | MSS | TCGA-DM-A0X9 |
4. Legacy临床数据获取
在Legacy数据库中可用的临床数据类型包括：
- Biospecimen data (Biotab format)：生物样本数据
- Tissue slide image (SVS format)：组织载玻片图像
- Clinical Supplement (XML format)：临床补充
- Pathology report (PDF)：病理报告
- Clinical data (Biotab format)：临床数据
-
Tissue slide image 获取
# Tissue slide image files library(TCGAbiolinks) library(SummarizedExperiment) query <- GDCquery(project = "TCGA-COAD", data.category = "Clinical", data.type = "Tissue slide image", legacy = TRUE, barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) query %>% getResults %>% datatable(options = list(scrollX = TRUE, keys = TRUE))data_release data_type tags file_name submitter_id file_id file_size cases state_comment id md5sum updated_datetime data_format access platform state version data_category type project code center_name center_short_name center_center_id center_namespace center_center_type tissue.definition 494 Tissue slide image image TCGA-RU-A8FL-01A-01-TSA.3743238D-C8AE-49A3-B5C9-3B18C1B64964.svs 530083be-6bdf-49e8-85dc-3c3ee5d5dcd5 186948553 TCGA-RU-A8FL 530083be-6bdf-49e8-85dc-3c3ee5d5dcd5 50b05bcaadce3553bb763a734f976316 2017-03-05T18:19:57.255497-06:00 SVS open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR 975 Tissue slide image image TCGA-AA-3972-01A-01-BS1.6c038157-503f-47dc-9445-72d7cdcae1a7.svs 0d4a3c6c-0ab2-44d2-9b08-90f5ea84555f 130569853 TCGA-AA-3972 0d4a3c6c-0ab2-44d2-9b08-90f5ea84555f 65d8fe397397d1fd633fd3279301310f 2017-03-05T18:32:29.523130-06:00 SVS open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR 980 Tissue slide image image TCGA-AA-3972-01A-01-TS1.3492c5d3-141f-48f9-a61b-48a1f595792c.svs 4966c8e3-37fd-4296-8a8a-216def9ec311 62750835 TCGA-AA-3972 4966c8e3-37fd-4296-8a8a-216def9ec311 18d8cc99e47b1522264f0f00cd4f85ca 2017-03-05T09:56:10.833727-06:00 SVS open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR -
Pathology report 获取
# Pathology report query <- GDCquery(project = "TCGA-COAD", data.category = "Clinical", data.type = "Pathology report", legacy = TRUE, barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) query %>% getResults %>% datatable(options = list(scrollX = TRUE, keys = TRUE))data_release data_type updated_datetime file_name submitter_id file_id file_size cases state_comment id md5sum data_format access platform state version data_category type project code center_name center_short_name center_center_id center_namespace center_center_type tissue.definition 8 Pathology report 2017-03-05T18:42:42.189892-06:00 TCGA-RU-A8FL.92DF9BB6-DB3F-40A7-AE1E-8272C46B1968.pdf a4753077-2bd3-4301-8424-b7575c8ccd66 206913 TCGA-RU-A8FL a4753077-2bd3-4301-8424-b7575c8ccd66 1c0cd3716d7c879d41d973282926c489 PDF open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR 307 Pathology report 2017-03-05T16:30:32.274191-06:00 TCGA-AA-3972.2562de97-b8b4-4547-9e7f-4c0fab6552b3.pdf b77a41e9-cf0d-4b94-9576-09e91b6d8f61 8658 TCGA-AA-3972 b77a41e9-cf0d-4b94-9576-09e91b6d8f61 626f8c94641ea67b6bc4b96de0ad4fd0 PDF open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR -
Clinical Supplement 获取
# Clinical Supplement query <- GDCquery(project = "TCGA-COAD", data.category = "Clinical", data.type = "Clinical Supplement", legacy = TRUE, barcode = c("TCGA-RU-A8FL","TCGA-AA-3972")) query %>% getResults %>% datatable(options = list(scrollX = TRUE, keys = TRUE))data_release data_type updated_datetime file_name submitter_id file_id file_size cases state_comment id created_datetime md5sum data_format access state version data_category type project tissue.definition 275 Clinical Supplement 2017-03-04T16:40:34.621217-06:00 nationwidechildrens.org_clinical.TCGA-RU-A8FL.xml 3c5a4713-6855-42d4-aed6-3129bfe80c58 62955 TCGA-RU-A8FL 3c5a4713-6855-42d4-aed6-3129bfe80c58 2016-05-04T08:54:03.280502-05:00 5f997f26c363f1d0727aaea5760b7c92 BCR XML open live Clinical clinical_supplement TCGA-COAD 427 Clinical Supplement 2017-03-04T16:40:34.621217-06:00 nationwidechildrens.org_clinical.TCGA-AA-3972.xml c76af5df-aab0-47a0-a543-77668be3f0c7 66578 TCGA-AA-3972 c76af5df-aab0-47a0-a543-77668be3f0c7 2016-05-04T08:54:13.372056-05:00 13edc34d65d52aa25b74dd9d769e1feb BCR XML open live Clinical clinical_supplement TCGA-COAD -
Clinical data 获取
# Clinical data query <- GDCquery(project = "TCGA-COAD", data.category = "Clinical", data.type = "Clinical data", legacy = TRUE, file.type = "txt") query %>% getResults %>% select(-matches("cases"))%>% datatable(options = list(scrollX = TRUE, keys = TRUE))data_release data_type tags file_name submitter_id file_id file_size state_comment id created_datetime md5sum updated_datetime data_format access platform state version data_category type project code center_name center_short_name center_center_id center_namespace center_center_type tissue.definition 23 Clinical data drug nationwidechildrens.org_clinical_drug_coad.txt 0415ffe2-a98d-40b9-ac60-6753fce56c7b 237163 0415ffe2-a98d-40b9-ac60-6753fce56c7b 2016-04-20T16:20:56.238694-05:00 dac877287ee1938fc69659127c02a151 2017-03-04T20:47:52.066809-06:00 Biotab open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR 25 Clinical data patient nationwidechildrens.org_clinical_patient_coad.txt b58b5947-d2b6-4cc7-9eff-cc0083d5bf4b 396060 b58b5947-d2b6-4cc7-9eff-cc0083d5bf4b 2016-04-20T16:20:56.238694-05:00 1f458eee1a95f3f45725e9881dcb1bf3 2017-03-05T11:00:22.460578-06:00 Biotab open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR 29 Clinical data radiation nationwidechildrens.org_clinical_radiation_coad.txt 36b48c2d-f45d-4995-bc2d-931f5c190919 6264 36b48c2d-f45d-4995-bc2d-931f5c190919 2016-04-20T16:20:56.238694-05:00 f8f2c8a4a8131fa4fb600ead81565c39 2017-03-05T11:47:51.010995-06:00 Biotab open Clinical live Clinical file TCGA-COAD 36 Nationwide Children's Hospital BCR NCH a6b3bcf1-9ca6-56e9-8f04-0e3a63e60a6a nationwidechildrens.org BCR -
Biospecimen data 获取
GDCdownload(query) clinical.biotab <- GDCprepare(query) names(clinical.biotab) ## [1] "clinical_radiation_coad" "clinical_nte_coad" ## [3] "clinical_patient_coad" "clinical_drug_coad" ## [5] "clinical_follow_up_v1.0_nte_coad" "clinical_omf_v4.0_coad" ## [7] "clinical_follow_up_v1.0_coad" datatable(clinical.biotab$clinical_radiation_coad, options = list(scrollX = TRUE, keys = TRUE))bcr_patient_uuid bcr_patient_barcode bcr_radiation_barcode bcr_radiation_uuid form_completion_date radiation_therapy_type radiation_therapy_site radiation_total_dose radiation_adjuvant_units radiation_adjuvant_fractions_total radiation_therapy_started_days_to radiation_therapy_ongoing_indicator radiation_therapy_ended_days_to treatment_best_response course_number radiation_type_other therapy_regimen therapy_regimen_other 1 bcr_patient_uuid bcr_patient_barcode bcr_radiation_barcode bcr_radiation_uuid form_completion_date radiation_type anatomic_treatment_site radiation_dosage units numfractions days_to_radiation_therapy_start radiation_treatment_ongoing days_to_radiation_therapy_end measure_of_response course_number radiation_type_notes regimen_indication regimen_indication_notes 2 CDE_ID: CDE_ID:2673794 CDE_ID: CDE_ID: CDE_ID: CDE_ID:2842944 CDE_ID:2793522 CDE_ID:2721441 CDE_ID:61446 CDE_ID:61465 CDE_ID:3008313 CDE_ID:2842745 CDE_ID:3008333 CDE_ID:2857291 CDE_ID:2732184 CDE_ID:2195477 CDE_ID:2793511 CDE_ID:2793516 3 e6ec5a68-7555-4f26-bd7e-9cdb4c5f7004 TCGA-AA-3549 TCGA-AA-3549-R38338 B72A855F-225F-4537-A74F-8485ABDBA0D0 2012-12-13 External Distant Recurrence 9 Gy [Not Available] 1126 NO 1126 Radiographic Progressive Disease [Not Available] [Not Applicable] [Not Available] [Not Available] 4 bce3ce45-4fb3-4d8e-9ec7-d24427c2ba4d TCGA-AA-3692 TCGA-AA-3692-R38345 2054309D-1EBC-4311-BF8A-621F6447F385 2012-12-13 External Distant Recurrence 39 Gy [Not Available] 31 NO 426 Radiographic Progressive Disease [Not Available] [Not Applicable] [Not Available] [Not Available] 5 bce3ce45-4fb3-4d8e-9ec7-d24427c2ba4d TCGA-AA-3692 TCGA-AA-3692-R38346 1081C34F-DA75-4856-966C-8F9B10E784AA 2012-12-13 External Distant Recurrence 38 Gy [Not Available] 365 NO 761 Radiographic Progressive Disease [Not Available] [Not Applicable] [Not Available] [Not Available] 只显示了部分数据
5. 临床数据不一致
在Clinical indexed的临床数据中发现了一些不一致的情况，并且正在由GDC团队进行调查。这些不一致是：
- Vital status（生命状态）字段未正确更新
- Tumor Grade（肿瘤等级）字段未填充
- Progression or Recurrence（进展或重复）字段未填充
5.1. Vital status不一致
# Get XML files and parse them
clin.query <- GDCquery(project = "TCGA-READ", data.category = "Clinical", file.type = "xml", barcode = "TCGA-F5-6702")
GDCdownload(clin.query)
clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient")
clinical.patient.followup <- GDCprepare_clinic(clin.query, clinical.info = "follow_up")
# Get indexed data
clinical.index <- GDCquery_clinic("TCGA-READ")
dplyr::select(clinical.patient,vital_status,days_to_death,days_to_last_followup) %>% datatable
| vital_status | days_to_death | days_to_last_followup | |
|---|---|---|---|
| 1 | Alive | 66 |
dplyr::select(clinical.patient.followup, vital_status,days_to_death,days_to_last_followup) %>% datatable
| vital_status | days_to_death | days_to_last_followup | |
|---|---|---|---|
| 1 | Dead | 869 | |
| 2 | Alive | 452 |
# Vital status should be the same in the follow up table
dplyr::filter(clinical.index,submitter_id == "TCGA-F5-6702") %>% dplyr::select(vital_status,days_to_death,days_to_last_follow_up) %>% datatable
| vital_status | days_to_death | days_to_last_follow_up | |
|---|---|---|---|
| 1 | alive | 869 | 452 |
5.2. Progression or Recurrence 和 Tumor Grade 不一致
# Get XML files and parse them
recurrent.samples <- GDCquery(project = "TCGA-LIHC",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts",
sample.type = "Recurrent Solid Tumor")$results[[1]] %>% select(cases)
recurrent.patients <- unique(substr(recurrent.samples$cases,1,12))
clin.query <- GDCquery(project = "TCGA-LIHC", data.category = "Clinical", file.type = "xml", barcode = recurrent.patients)
GDCdownload(clin.query)
clinical.patient <- GDCprepare_clinic(clin.query, clinical.info = "patient")
# Get indexed data
GDCquery_clinic("TCGA-LIHC") %>% dplyr::filter(submitter_id %in% recurrent.patients) %>%
dplyr::select(progression_or_recurrence,days_to_recurrence,tumor_grade) %>% datatable
| progression_or_recurrence | days_to_recurrence | tumor_grade | |
|---|---|---|---|
| 1 | not reported | not reported | |
| 2 | not reported | not reported |
# XML data
clinical.patient %>% dplyr::select(bcr_patient_barcode,neoplasm_histologic_grade) %>% datatable
| bcr_patient_barcode | neoplasm_histologic_grade | |
|---|---|---|
| 1 | TCGA-DD-AACA | G3 |
| 2 | TCGA-ZS-A9CF | G2 |
6. 临床数据过滤功能
此外，还提供了一些处理临床数据的功能。
例如，函数TCGAquery_SampleTypes将根据参数typesample的类型过滤Barcodes。
| Argument | Description | |
|---|---|---|
| barcode | is a list of samples as TCGA barcodes | |
| typesample | a character vector indicating tissue type to query. Example: | |
| TP | PRIMARY SOLID TUMOR | |
| TR | RECURRENT SOLID TUMOR | |
| TB | Primary Blood Derived Cancer-Peripheral Blood | |
| TRBM | Recurrent Blood Derived Cancer-Bone Marrow | |
| TAP | Additional-New Primary | |
| TM | Metastatic | |
| TAM | Additional Metastatic | |
| THOC | Human Tumor Original Cells | |
| TBM | Primary Blood Derived Cancer-Bone Marrow | |
| NB | Blood Derived Normal | |
| NT | Solid Tissue Normal | |
| NBC | Buccal Cell Normal | |
| NEBV | EBV Immortalized Normal | |
| NBM | Bone Marrow Normal |
该函数TCGAquery_MatchedCoupledSampleTypes将从全部样本中过滤获得typesample类型的样本。例如，如果将TP和TR设置为typesample，则该函数将返回对应患者的条形码（如果它具有两种类型）。因此，如果患者有TP而但没有TR，则不会返回条形码。如果患者有TP和TR，则返回两个条形码。
案例：
bar <- c("TCGA-G9-6378-02A-11R-1789-07", "TCGA-CH-5767-04A-11R-1789-07",
"TCGA-G9-6332-60A-11R-1789-07", "TCGA-G9-6336-01A-11R-1789-07",
"TCGA-G9-6336-11A-11R-1789-07", "TCGA-G9-7336-11A-11R-1789-07",
"TCGA-G9-7336-04A-11R-1789-07", "TCGA-G9-7336-14A-11R-1789-07",
"TCGA-G9-7036-04A-11R-1789-07", "TCGA-G9-7036-02A-11R-1789-07",
"TCGA-G9-7036-11A-11R-1789-07", "TCGA-G9-7036-03A-11R-1789-07",
"TCGA-G9-7036-10A-11R-1789-07", "TCGA-BH-A1ES-10A-11R-1789-07",
"TCGA-BH-A1F0-10A-11R-1789-07", "TCGA-BH-A0BZ-02A-11R-1789-07",
"TCGA-B6-A0WY-04A-11R-1789-07", "TCGA-BH-A1FG-04A-11R-1789-08",
"TCGA-D8-A1JS-04A-11R-2089-08", "TCGA-AN-A0FN-11A-11R-8789-08",
"TCGA-AR-A2LQ-12A-11R-8799-08", "TCGA-AR-A2LH-03A-11R-1789-07",
"TCGA-BH-A1F8-04A-11R-5789-07", "TCGA-AR-A24T-04A-55R-1789-07",
"TCGA-AO-A0J5-05A-11R-1789-07", "TCGA-BH-A0B4-11A-12R-1789-07",
"TCGA-B6-A1KN-60A-13R-1789-07", "TCGA-AO-A0J5-01A-11R-1789-07",
"TCGA-AO-A0J5-01A-11R-1789-07", "TCGA-G9-6336-11A-11R-1789-07",
"TCGA-G9-6380-11A-11R-1789-07", "TCGA-G9-6380-01A-11R-1789-07",
"TCGA-G9-6340-01A-11R-1789-07", "TCGA-G9-6340-11A-11R-1789-07")
S <- TCGAquery_SampleTypes(bar,"TP")
S2 <- TCGAquery_SampleTypes(bar,"NB")
# Retrieve multiple tissue types NOT FROM THE SAME PATIENTS
SS <- TCGAquery_SampleTypes(bar,c("TP","NB"))
# Retrieve multiple tissue types FROM THE SAME PATIENTS
SSS <- TCGAquery_MatchedCoupledSampleTypes(bar,c("NT","TP"))
7. 其他有用的代码
要获取TGCA样本的所有信息，您可以使用以下脚本：
# This code will get all clinical indexed data from TCGA
library(data.table)
library(dplyr)
library(regexPipes)
clinical <- TCGAbiolinks:::getGDCprojects()$project_id %>%
regexPipes::grep("TCGA",value=T) %>%
sort %>%
plyr::alply(1,GDCquery_clinic, .progress = "text") %>%
rbindlist
readr::write_csv(clinical,path = paste0("all_clin_indexed.csv"))
# This code will get all clinical XML data from TCGA
getclinical <- function(proj){
message(proj)
while(1){
result = tryCatch({
query <- GDCquery(project = proj, data.category = "Clinical",file.type = "xml")
GDCdownload(query)
clinical <- GDCprepare_clinic(query, clinical.info = "patient")
for(i in c("admin","radiation","follow_up","drug","new_tumor_event")){
message(i)
aux <- GDCprepare_clinic(query, clinical.info = i)
if(is.null(aux) || nrow(aux) == 0) next
# add suffix manually if it already exists
replicated <- which(grep("bcr_patient_barcode",colnames(aux), value = T,invert = T) %in% colnames(clinical))
colnames(aux)[replicated] <- paste0(colnames(aux)[replicated],".",i)
if(!is.null(aux)) clinical <- merge(clinical,aux,by = "bcr_patient_barcode", all = TRUE)
}
readr::write_csv(clinical,path = paste0(proj,"_clinical_from_XML.csv")) # Save the clinical data into a csv file
return(clinical)
}, error = function(e) {
message(paste0("Error clinical: ", proj))
})
}
}
clinical <- TCGAbiolinks:::getGDCprojects()$project_id %>%
regexPipes::grep("TCGA",value=T) %>% sort %>%
plyr::alply(1,getclinical, .progress = "text") %>%
rbindlist(fill = TRUE) %>% setDF %>% subset(!duplicated(clinical))
readr::write_csv(clinical,path = "all_clin_XML.csv")
# result: https://drive.google.com/open?id=0B0-8N2fjttG-WWxSVE5MSGpva1U
# Obs: this table has multiple lines for each patient, as the patient might have several followups, drug treatments,
# new tumor events etc...
更新时间：2019-05-25 17:18:18
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原文链接：https://blog.computsystmed.com/archives/translation-tcgabiolinks-clinical-data
最后更新：2019-05-25 17:18:18
