diff --git a/scripts/data_guide/Dockerfile b/scripts/data_guide/Dockerfile index 630481e..569a2de 100644 --- a/scripts/data_guide/Dockerfile +++ b/scripts/data_guide/Dockerfile @@ -1,9 +1,9 @@ -FROM r-base:4.2.2 +FROM r-base:4.3.1 # These will allow for the renv install -ENV RENV_VERSION 0.16.0 +ENV RENV_VERSION 1.0.7 ENV RENV_PATHS_LIBRARY renv/library -ENV QUARTO_VERSION 1.3.433 +ENV QUARTO_VERSION 1.4.555 RUN apt-get update && apt-get -y install \ libpng-dev \ @@ -27,7 +27,7 @@ RUN apt-get update && apt-get -y install \ rm -rf /var/lib/apt/lists/* RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))" -RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')" +RUN R -e "remotes::install_github('rstudio/renv@v${RENV_VERSION}')" WORKDIR /data_guide # only copy renv file @@ -37,7 +37,7 @@ RUN R -e "renv::restore()" # Must install quarto cli WORKDIR /opt -RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.tar.gz +RUN wget "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.tar.gz" RUN tar -C /opt -xvzf quarto-${QUARTO_VERSION}-linux-amd64.tar.gz # Set quarto path diff --git a/scripts/data_guide/README.md b/scripts/data_guide/README.md index 6591462..15bc5b3 100644 --- a/scripts/data_guide/README.md +++ b/scripts/data_guide/README.md @@ -1,3 +1,10 @@ # Updating the data guide Add or update your information for your site into the dedicated field and then submit a pull request. + + +## Run the command + +``` +Rscript generate_data_guide_cli.R 16.6-consortium syn3380222 +``` \ No newline at end of file diff --git a/scripts/data_guide/data_guide.qmd b/scripts/data_guide/data_guide.qmd index 1465791..86b070d 100644 --- a/scripts/data_guide/data_guide.qmd +++ b/scripts/data_guide/data_guide.qmd @@ -134,7 +134,7 @@ AACR Project GENIE data versions follow a numbering scheme derived from [semanti AACR Project GENIE Data is currently available via two mechanisms: -- Synapse Platform (Sage Bionetworks): https://synapse.org/genie +- Synapse Platform (Sage Bionetworks): https://genie.synapse.org/ or https://synapse.org/genie - cBioPortal for Cancer Genomics (MSK): https://www.cbioportal.org/genie/ @@ -144,7 +144,7 @@ All users of the AACR Project GENIE data must agree to the following terms of us - Users will not attempt to identify or contact individual participants from whom these data were collected by any means. -- Users will not redistribute the data without express written permission from the AACR Project GENIE Coordinating Center (send email to: info\@aacrgenie.org). +- Users will not redistribute the data without express written permission from the AACR Project GENIE Coordinating Center (send email to: genieinfo\@aacr.org). When publishing or presenting work using or referencing the AACR Project GENIE dataset please include the following attributions: @@ -202,7 +202,7 @@ The GENIE dataset is generated from data curated by multiple cancer centers. Eac Only validated files that adhere to the submission guidelines will be pushed to the release. The files that do not pass these validation checks will not be processed and an email notifying any errors or warnings will be sent to each center to correct. Each accepted file type has its own submission guidelines the centers must follow. Some examples of these validation checks are given below: -- assay information file: `SEQ_ASSAY_ID`s must start with center abbreviation. +- assay information file: `SEQ_ASSAY_ID`s must start with the center abbreviation. - BED file: `Start_Position` must only be integers and is the 2nd column. - MAF file: `T_ALT_COUNT` must be an integer. @@ -218,7 +218,7 @@ Samples from every major release and its associated consortium releases are vett [No BED file]{.underline} -Samples that have a `SEQ_ASSAY_ID` that don't have a bed file associated with them will be removed. +Samples that have a `SEQ_ASSAY_ID`, but don't have a bed file associated with them will be removed. [Oncotree]{.underline} @@ -230,16 +230,16 @@ Any sample with `SAMPLE_CLASS` that is cfDNA is removed from the public release. [Patient and sample retractions]{.underline} -- Implicit retraction occurs when any data that is has been withdrawn from new uploads will automatically be removed from the upcoming consortium/public releases. -- Explicit retractions occurs when centers submit a patient or sample ID in their retraction file. This may occur when a patient decides to retract their consent. +- Implicit retraction occurs when data removed from new uploads is automatically excluded from future releases. +- Explicit retraction occurs when centers submit a retraction file containing a patient or sample ID, often due to a patient's decision to withdraw their consent. [Age information redaction]{.underline} -When `AGE_AT_SEQ_REPORT`, `INT_CONTACT`, or `INT_DOD` is >32485 or <6570, the fields `BIRTH_YEAR`, `YEAR_CONTACT`, `YEAR_DEATH`, `INT_CONTACT`, `INT_DOD`, and `AGE_AT_SEQ_REPORT` are redacted. If the difference between the `BIRTH_YEAR` and `YEAR_CONTACT` or `BIRTH_YEAR` and `YEAR_DEATH` is greater than 89, those values will be redacted. +When `AGE_AT_SEQ_REPORT`, `INT_CONTACT`, or `INT_DOD` is \>32485 or <6570 days, the fields `BIRTH_YEAR`, `YEAR_CONTACT`, `YEAR_DEATH`, `INT_CONTACT`, `INT_DOD`, and `AGE_AT_SEQ_REPORT` are redacted. If the difference between the `BIRTH_YEAR` and `YEAR_CONTACT` or `BIRTH_YEAR` and `YEAR_DEATH` is greater than 89 years, those values will be redacted. -- Intervals are redacted with ">32485" and "<6570" -- Ages are redacted with ">89" and "<18" -- Years are redacted with "cannotReleaseHIPAA" and "withheld". +- Intervals are redacted with "\>32485" and "<6570" +- Ages are redacted with "\>89" and "<18" +- Years are marked as "cannotReleaseHIPAA" for individuals over 89 and as "withheld" for individuals under 18 ## Variant Data Filters @@ -269,20 +269,20 @@ Samples that have variants that could be merged together will be filtered out. T [Genome Nexus Annotation Status]{.underline} -Variants that are unable to be annotated by Genome Nexus are removed. +Mutation data that fails to be annotated by Genome-Nexus is excluded from the release. For example, this occurs when the allele extracted from the VCF or MAF file does not match the reference allele, or when the VEP tool that Genome-Nexus uses is unable to annotate the data. ## Processing Transformations -[Genome Nexus Annotation Pipeline]{.underline} +[Genome Nexus Annotation Pipeline]{.underline}: https://genie.genomenexus.org/ - Contributing GENIE centers provided mutation data in Variant Call Format (VCF) or Mutation Annotation Format (GDC MAF v1.0.0) with additionalfields for read counts supporting variant alleles, reference alleles, and total depth. Some "MAF-like" text files with minimal required columns were also received from the participating centers. These various input formats were converted into a complete tab-separated MAF format, with Genome Nexus. - The GENIE dataset is annotating all variants with Genome Nexus starting from the 9.1-consortium release (instead of vcf2maf). [Gene symbol harmonization]{.underline} -All submitted HUGO gene symbols will be harmonized against GRCh37 by checking the coordinates against the annotation. The below diagram illustrates how conflicts between submitted and harmonized symbols will be resolved. +All submitted HUGO gene symbols will be harmonized against GRCh37 by checking the coordinates against the annotation. -- Every single row of your bed file will be matched against the gene database. If the submitted symbol matches a row in the gene database and there is an overlap from the submitted bed region, the submitted symbol will be returned. +- Every single row of the bed file will be matched against the gene database. If the submitted symbol matches a row in the gene database and there is an overlap from the submitted bed region, the submitted symbol will be returned. - If the submitted symbol does not exist in the database or there is not any overlap, an attempt to find any gene that completely encapsulates the submitted bed region is made. If the bed region is contained completely inside one gene, then it is labelled as that gene. If a bed region is enclosed completely in more than one gene, and the submitted symbol doesn't match any of the genes returned, NULL will be returned. - If the submitted region isn't enclosed in any gene, then calculations are made to check if the bed region resides at least 90% in a gene. If there is more than one gene returned while doing 90% boundary calculations, NULL is returned. @@ -297,7 +297,7 @@ On a per site basis, if there are more two rows that are the same gene, the valu [Clinical Tier Release Scope Filters]{.underline} -Some parts of the clinical data is masked from the public releases. This is based on a clinical tier release scope of release document. +Some parts of the clinical data is masked from the public releases. This is based on a clinical tier release scope of release document determined by the consortium. ## Post-Release Quality Checks @@ -317,13 +317,14 @@ The resulting set is annotated with a fisher p-value for the variants that pass After release, each center performs a manual review of their data based on an auto-generated dashboard that summarizes some key elements. Some examples of items sites review are given below: -- Confirm sample count +- Confirm sample count. - Confirm variant count (flagged mutations). Most of these variants are potential artifacts flagged by manual review of cBioPortal. Suggestions for variants that should be part of this list or any variant shouldn't be part of this list are welcome. -- Fix BED and assay information discrepancies -- Confirm top 5 most frequently mutated genes per pipeline for all non-synonymous mutations -- Remove blacklisted variants -- Confirm clinical attribute distributions/values are valid -- Confirm patients and samples that were marked for retraction +- Fix BED and assay information discrepancies. +- Confirm top 5 most frequently mutated genes per pipeline for all non-synonymous mutations. +- Remove blacklisted variants. +- Confirm clinical attribute distributions/values are valid. +- Confirm patients and samples that were marked for retraction. +- Review failed annotations flagged by Genome-Nexus. # Summary of Sequence Pipeline @@ -431,29 +432,29 @@ for (center in sort(processed_centers)) { Description on most of the data files can be found in the [cBioPortal file formats](https://docs.cbioportal.org/file-formats) docs. -data_mutations_extended.txt +[data_mutations_extended.txt]{.underline} -* Description: The mutation data file extends the Mutation Annotation Format (MAF) created as part of the Cancer Genome Atlas project, by adding extra annotations to each mutation record. +* Description: The mutation data file expands the Mutation Annotation Format (MAF) developed by the Cancer Genome Atlas project by including additional annotations for each mutation record. * Details: [MAF format](https://docs.cbioportal.org/file-formats/#mutation-data) -data_clinical_patient.txt/data_clinical_sample.txt +[data_clinical_patient.txt/data_clinical_sample.txt]{.underline} -* Description: The clinical data is used to capture both clinical attributes and the mapping between patient and sample IDs. +* Description: The clinical data file is used to capture both clinical attributes and the mapping between patient and sample IDs. * Details: [Clinical format](https://docs.cbioportal.org/file-formats/#clinical-data) -data_CNA.txt +[data_CNA.txt]{.underline} * Description: The copy number data file contain values that would be derived from copy-number analysis algorithms like GISTIC or RAE. GISTIC can be installed or run online using the GISTIC 2.0 module on GenePattern. * Details: [CNA format](https://docs.cbioportal.org/file-formats/#discrete-copy-number-data) -data_sv.txt +[data_sv.txt]{.underline} * Description: The structural variant file contains information on structural variants. This file format replaces the deprecated data_fusions.txt file format. * Details: [Structural Variant format](https://docs.cbioportal.org/file-formats/#structural-variant-data) -genomic_information.txt +[genomic_information.txt]{.underline} -* Description: The genomic information file describes genomic coordinates covered by all platforms contributed to GENIE. This is used for the MAF and in BED filter, and generating gene panel files. +* Description: The genomic information file describes genomic coordinates covered by all platforms contributed to GENIE. This is used in the inBED filter and to generate gene panel files. * `Chromosome`, `Start_Position`, `End_Position`: Gene positions * `Hugo_Symbol`: Re-mapped gene symbol based on gene positions * `ID`: Center submitted gene symbols @@ -461,164 +462,205 @@ genomic_information.txt * `includeInPanel`: Used to define gene panel files for cBioPortal. * `clinicalReported`: These are the genes that were clinically Reported. Blank means information not provided. -assay_information.txt +[assay_information.txt]{.underline} -* Description: This describes the genomic profile information for each assay and is used to auto write the summary of pipeline section of the data guide. +* Description: This describes the genomic profile information for each assay and is used to auto write the Summary of Sequence Pipeline section of the data guide. * Details: This is not a cBioPortal file format - * `is_paired_end`, `library_selection`, `library_strategy`, `platform`, `read_length`, target_capture_kit, instrument_model: defined by [GDC read group](https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group) - * `number_of_genes`: Number of genes from which variants are called + * `SEQ_ASSAY_ID`: The assay identifier for the genomic testing platform + * `is_paired_end`, `library_selection`, `library_strategy`, `platform`, `read_length`, `target_capture_kit`, `instrument_model`: defined by [GDC read group](https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group) + * `number_of_genes`: Number of genes from which variants are called. * `variant_classifications`: List of types of variants that are reported for this assay. * `gene_padding`: Number of base pairs to add to exon endpoints for the inBED filter. - * `alteration_types`: List of alteration types. specimen_type: List of specimen types. - * `specimen_tumor_cellularity`: Tumor Cellularity Cutoff + * `alteration_types`: List of alteration types. + * `preservation_technique`: Either FFPE, fresh_frozen, or NA. + * `specimen_tumor_cellularity`: Tumor Cellularity Cutoff. * `calling_strategy`: Tumor only or tumor normal. - * `coverage`: List of coverage + * `coverage`: List of coverage types. + * `SEQ_PIPELINE_ID`: For those centers that have multiple panels per assay (multiple `SEQ_ASSAY_ID`s) -data_cna_hg19.seg +[data_cna_hg19.seg]{.underline} -* Description: A SEG file (segmented data; .seg or .cbs) is a tab-delimited text file that lists loci and associated numeric values. +* Description: A SEG file (segmented data; .seg or .cbs) is a tab-delimited text file that lists loci and associated numeric values. The segmented data file format is the output of the Circular Binary Segmentation algorithm (Olshen et al., 2004). * Details: [SEG format](https://docs.cbioportal.org/file-formats/#segmented-data) -data_gene_matrix.txt +[data_gene_matrix.txt]{.underline} * Description: This file contains a mapping between `SAMPLE_ID` and `SEQ_ASSAY_ID`. This assumes the type of genomic data extracted for the sample based on the associated SEQ_ASSAY_ID. * Details: [Gene Matrix format](https://docs.cbioportal.org/file-formats/#gene-panel-matrix-file) -data_gene_panel_* files +[data_gene_panel_* files]{.underline} -* Description: Gene panel functionality can specify which genes are assayed on a panel and assign samples and genetic profiles (such as mutation data) to a panel. +* Description: These files specify which genes are assayed on a panel and assign samples and genetic profiles (such as mutation data) to a panel. * Details: [Gene panel format](https://docs.cbioportal.org/file-formats/#gene-panel-data) -release_notes.pdf +[release_notes.pdf]{.underline} -* Description: Detailed release notes for the release. +* Description: Detailed release notes for each release. -meta_* files +[meta_* files]{.underline} * Description: Metadata files required for import into cBioPortal. * Details: Each cBioPortal file format has an associated meta file. -case_lists files +[case_lists files]{.underline} * Description: Case lists are used to define sample lists that can be selected on the query page. Each case list file has the naming format cases_{type}.txt and is located in the case_lists folder found under each GENIE release. * Details: [Case list format](https://docs.cbioportal.org/file-formats/#case-lists) + +# Description of Clinical Data Fields - +[data_clinical_patient.txt]{.underline} -# Clinical Data +`PATIENT_ID` -`AGE_AT_SEQ_REPORT` +* Expected Values: GENIE-[CENTER]-[patient identifier] +* Data Description: The unique, anonymized patient identifier for the GENIE project. The first component is the string, "GENIE"; the second component is the Center abbreviation. The third component is an anonymized unique identifier for the patient. -* Expected Values: [Integer], <18, >89, Unknown -* Data Description: The age of the patient at the time that the sequencing results were reported. Age is masked for patients aged 90 years and greater and for patients under 18 years. +`SEX` -`CENTER` +* Expected Values: Female, Male, Other, Transsexual, Not Collected, Unknown +* Data Description: The patient's sex code; this data element derives from NAACCR v16, Element #220. + +`PRIMARY_RACE` + +* Expected Values: Asian, Black, Native American, Not Applicable, Not Collected, Other, Unknown, Pacific Islander, White +* Data Description: The primary race recorded for the patient; this data element derives from NAACCR v16, Element #160. For institutions collecting more than one race category, this race code is the primary race for the patient. Institutions not collecting race have set this field to Not Collected. + +`SECONDARY_RACE` [Not available for public releases] + +* Expected Values: Asian, Black, Native American, Not Applicable, Not Collected, Other, Unknown, Pacific Islander, White +* Data Description: The secondary race recorded for the patient; this data element derives from NAACCR v16, Element #161. Institutions not collecting race have set this field to Not Collected. + +`TERTIARY_RACE` [Not available for public releases] -* Expected Values: MSK -* Data Description: The center submitting the clinical and genomic data +* Expected Values: Asian, Black, Native American, Not Applicable, Not Collected, Other, Unknown, Pacific Islander, White +* Data Description: The tertiary race recorded for the patient; this data element derives from NAACCR v16, Element #162. Institutions not collecting race have set this field to Not Collected. `ETHNICITY` * Expected Values: Non-Spanish/non-Hispanic, Spanish/Hispanic, Unknown, Not Collected -* Data Description: Indication of Spanish/Hispanic origin of the patient; this data element maps to the NAACCR v16, Element #190. Institutions not collecting Spanish/Hispanic origin have set this column to Unknown. +* Data Description: Indication of Spanish/Hispanic origin of the patient; this data element derives from NAACCR v16, Element #190. Institutions not collecting Spanish/Hispanic origin have set this column to Not Collected. -`ONCOTREE_CODE` +`BIRTH_YEAR` [Not available for public releases] -* Expected Values: Values can be explored here: - http://oncotree.mskcc.org/#/home?version=`r strsplit(oncotree_link, "=")[[1]][2]` -* Data Description: The primary cancer diagnosis "main type", based on the OncoTree ontology. The version of Oncotree ontology that was used for this release is `r strsplit(oncotree_link, "=")[[1]][2]`. +* Expected Values: [Integer], Unknown, cannotReleaseHIPAA, withheld +* Data Description: The four-digit year corresponding to the patient's birth date. -`PATIENT_ID` +`CENTER` -* Expected Values: GENIE-JHU-1234 -* Data Description: The unique, anonymized patient identifier for the GENIE project. Conforms to the following the convention: GENIE-CENTER-1234. The first component is the string, "GENIE"; the second component is the Center abbreviation. The third component is an anonymized unique identifier for the patient. +* Expected Values: The center abbreviation (e.g. MSK, DFCI, UHN) +* Data Description: The center submitting the clinical and genomic data. -`PRIMARY_RACE` +`INT_CONTACT` -* Expected Values: Asian, Black, Native American, Not Applicable, Not Collected, Other, Unknown, Pacific Islander, White -* Data Description: The primary race recorded for the patient; this data element maps to the NAACCR v16, Element #160. For institutions collecting more than one race category, this race code is the primary race for the patient. Institutions not collecting race have set this field to Unknown. +* Expected Values: [Integer], <6570, >32485, Not Collected, Not Released, Unknown +* Data Description: Interval in days from date of birth (DOB) to date of last contact. -`SAMPLE_ID` +`INT_DOD` -* Expected Values: GENIE-JHU-1234-9876 -* Data Description: The unique, anonymized sample identifier for the GENIE project. Conforms to the following the convention: GENIE-CENTER-1234-9876. The first component is the string, "GENIE"; the second component is the Center abbreviation. The third component is an anonymized, unique patient identifier. The fourth component is a unique identifier for the sample that will distinguish between two or more specimens from a single patient. +* Expected Values: [Integer], <6570, >32485, Not Collected, Not Released, Not Applicable, Unknown +* Data Description: Interval in days from date of birth (DOB) to date of death (DOD). -`SAMPLE_TYPE` +`YEAR_CONTACT` -* Expected Values: Primary, Metastasis, Unspecified, Not Applicable or Heme, Not Collected -* Data Description: The specimen's type including primary, metastasis and etc... +* Expected Values: [Integer], <18, >89, Not Collected, Not Released, Unknown +* Data Description: Record of the year the patient is last known to be alive, as determined from electronic health records (EHR), tumor registries, or other relevant systems. -`SAMPLE_TYPE_DETAILED` +`YEAR_DEATH` -* Expected Values: Primary tumor, Lymph node metastasis -* Data Description: The specimen's detailed type based on its location, including primary site, site of local recurrence, distant metastasis or hematologic malignancy. +* Expected Values: [Integer], <18, >89, Not Collected, Not Released, Not Applicable, Unknown +* Data Description: Year of death. -`SEQ_ASSAY_ID` +`DEAD` -* Expected Values: DFCI-ONCOPANEL-1 -* Data Description: The institutional assay identifier for genomic testing platform. Components are separated by hyphens, with the first component corresponding to the Center's abbreviation. All specimens tested by the same platform should have the same identifier. +* Expected Values: TRUE, FALSE, Not Collected, Not Released, Not Applicable, Unknown +* Data Description: The patient's vital status. -`SEX` +[data_clinical_sample.txt]{.underline} -* Expected Values: Female, Male, Other, Transsexual, Not Collected, Unknown -* Data Description: The patient's sex code; this data element maps to the NAACCR v16, Element #220. +`SAMPLE_ID` -`CANCER_TYPE` +* Expected Values: GENIE-[CENTER]-[patient identifier]-[sample identifer] +* Data Description: The unique, anonymized sample identifier for the GENIE project. The first component is the string, "GENIE"; the second component is the Center abbreviation. The third component is an anonymized, unique patient identifier. The fourth component is a unique identifier for the sample that will distinguish between two or more specimens from a single patient. -* Expected Values: Non-Small Cell Lung Cancer -* Data Description: The primary cancer diagnosis "main type", based on the OncoTree ontology. For example, the OncoTree code of LUAD maps to: "Non-Small Cell Lung Cancer". The version of Oncotree ontology that was used for this release is `r strsplit(oncotree_link, "=")[[1]][2]`. +`AGE_AT_SEQ_REPORT` -`CANCER_TYPE_DETAILED` +* Expected Values: [Integer], <18, >89, Unknown +* Data Description: The age of the patient at the time that the sequencing results were reported. -* Expected Values: Lung Adenocarcinoma -* Data Description: The primary cancer diagnosis label, based on the OncoTree ontology. For example, the OncoTree code of LUAD maps to the label: "Lung Adenocarcinoma (LUAD)". The version of Oncotree ontology that was used for this release is `r strsplit(oncotree_link, "=")[[1]][2]`. +`AGE_AT_SEQ_REPORT_DAYS` [Not available for public releases] -`YEAR_CONTACT` +* Expected Values: [Integer], >32485, <6570, Unknown +* Data Description: The interval in days between the patient's date of birth and the date of the sequencing report that is associated with the sample. The interval is masked for >32485 and <6570. -* Expected Values: [Integer], <18, >89, Not Collected, Not Released, Unknown -* Data Description: Record of the year that the patient is last known to be alive - data to be derived from information including and EHR, tumor registry, or other system. +`ONCOTREE_CODE` -`YEAR_DEATH` +* Expected Values: + http://oncotree.mskcc.org/#/home?version=`r strsplit(oncotree_link, "=")[[1]][2]` +* Data Description: The primary cancer diagnosis, or "main type", classified based on the OncoTree ontology. The version of the OncoTree ontology used for this release is `r strsplit(oncotree_link, "=")[[1]][2]`. -* Expected Values: [Integer], <18, >89, Not Collected, Not Released, Not Applicable, Unknown -* Data Description: Year of death. +`SAMPLE_TYPE` -`INT_CONTACT` +* Expected Values: Primary, Metastasis, Unspecified, Not Applicable or Heme, Not Collected +* Data Description: The specimen's sample type based on its location. -* Expected Values: [Integer], <6570, >32485, Not Collected, Not Released, Unknown -* Data Description: Interval in days from DOB to date of last contact. +`SAMPLE_TYPE_DETAILED` -`INT_DOD` +* Expected Values: Primary tumor, Metastasis site unspecified, Local recurrence, Lymph node metastasis, Not applicable or hematologic malignancy, Distant organ metastasis, Not Collected, Not otherwise specified +* Data Description: The specimen's detailed sample type based on its location. -* Expected Values: [Integer], <6570, >32485, Not Collected, Not Released, Not Applicable, Unknown -* Data Description: Interval in days from DOB to DOD. +`SEQ_ASSAY_ID` -`DEAD` +* Expected Values: [Center]-[Panel] +* Data Description: The institutional assay identifier for genomic testing platform. Components are separated by hyphens, with the first component corresponding to the Center's abbreviation. All specimens tested by the same platform should have the same identifier. -* Expected Values: TRUE, FALSE, Not Collected, Not Released, Not Applicable, Unknown -* Data Description: Is this patient known to be deceased? +`CANCER_TYPE` -`BIRTH_YEAR` [Not available for public releases] +* Expected Values: Non-Small Cell Lung Cancer (example) + http://oncotree.mskcc.org/#/home?version=`r strsplit(oncotree_link, "=")[[1]][2]` +* Data Description: The primary cancer diagnosis label, or "main type", based on the OncoTree ontology. For example, the OncoTree code of LUAD maps to: “Non-Small Cell Lung Cancer”. -* Expected Values: [Integer], Unknown, cannotReleaseHIPAA, withheld -* Data Description: The four-digit year associated with the patient's date of birth. +`CANCER_TYPE_DETAILED` + +* Expected Values: Lung Adenocarcinoma (example) + http://oncotree.mskcc.org/#/home?version=`r strsplit(oncotree_link, "=")[[1]][2]` +* Data Description: The detailed primary cancer diagnosis label based on the OncoTree ontology. For example, the OncoTree code of LUAD maps to the label: "Lung Adenocarcinoma (LUAD)". `SAMPLE_CLASS` [Not available for public releases] * Expected Values: Tumor, cfDNA -* Data Description: Annotate samples as Tumor or cfDNA samples. cfDNA samples are not available for public releases. +* Data Description: This sample category of either Tumor or circulating cell-free DNA (cfDNA) type. cfDNA samples are filtered out in public releases. `SEQ_YEAR` [Not available for public releases] * Expected Values: [Integer] -* Data Description: Each record has a year of sequencing. +* Data Description: The year the sample was sequenced. -`AGE_AT_SEQ_REPORT_DAYS` [Not available for public releases] -* Expected Values: [Integer], >32485, <6570, Unknown -* Data Description: The interval in days between the patient's date of birth and the date of the sequencing report that is associated with the sample. The interval is masked for >32485 and <6570. +### Linking clinical data to genomic data + +* Link between `data_clinical_patient.txt` and `data_clinical_sample.txt`: + * Column in `data_clinical_patient.txt`: PATIENT_ID + * Column in `data_clinical_sample.txt`: PATIENT_ID + +* Link between `data_clinical_sample.txt` and `data_mutations_extended.txt`: + * Column in `data_clinical_sample.txt`: SAMPLE_ID + * Column in `data_mutations_extended.txt`: Tumor_Sample_Barcode + +* Link between `data_clinical_sample.txt` and `data_sv.txt`: + * Column in `data_clinical_sample.txt`: SAMPLE_ID + * Column in `data_sv.txt`: Tumor_Sample_Barcode + +* Link between `data_clinical_sample.txt` and `genie_data_cna_hg19.seg`: + * Column in `data_clinical_sample.txt`: SAMPLE_ID + * Column in `genie_data_cna_hg19.seg`: ID + +* Link between `data_clinical_sample.txt` and `genomic_information.txt`: + * Column in `data_clinical_sample.txt`: SEQ_ASSAY_ID + * Column in `genomic_information.txt`: SEQ_ASSAY_ID + ### Center Strategies for OncoTree Assignment @@ -680,3 +722,5 @@ For center abbreviations please see Table 1. +------------------+-----------------------------------------------------------------+ | VCF | Variant Call Format | +------------------+-----------------------------------------------------------------+ +| SV | Structural variants | ++------------------+-----------------------------------------------------------------+ \ No newline at end of file diff --git a/scripts/data_guide/genomic_profiles/chop.qmd b/scripts/data_guide/genomic_profiles/chop.qmd index f74b3c0..967d8f9 100644 --- a/scripts/data_guide/genomic_profiles/chop.qmd +++ b/scripts/data_guide/genomic_profiles/chop.qmd @@ -1,4 +1,4 @@ -### [Chilrden's Hospital of Philadelphia](https://www.chop.edu/) (CHOP) +### [Children's Hospital of Philadelphia](https://www.chop.edu/) (CHOP) The CHOP Comprehensive Solid Tumor Panel and Comprehensive Hematologic Cancer Pane include sequence and copy number analyses of 238 and 117 cancer genes, respectively, genotyping of two genes associated with cancer pharmacogenomics, and a Fusion Panel targeting over 700 exons of 117 cancer genes. diff --git a/scripts/data_guide/renv.lock b/scripts/data_guide/renv.lock index e2941e4..437ebac 100644 --- a/scripts/data_guide/renv.lock +++ b/scripts/data_guide/renv.lock @@ -1,6 +1,6 @@ { "R": { - 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