OSCR

High-dose furmonertinib as first-line treatment for untreated EGFR-mutated advanced NSCLC with central nervous system metastases: A phase 2 trial.

Code ↔ Paper

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  1. [1] § STAR★Methods › Method details › Bioinformatics analysis ↔ src/main/java/org/broadinstitute/hellbender/tools/funcotator/mafOutput/MafOutputRendererConstants.java, lines 180–266 · score 0.62 · gene fusions, database, Somatic, Chromosomal, BAM, strand
  2. [2] § STAR★Methods › Quantification and statistical analysis ↔ src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java, lines 119–181 · score 0.56 · Wilcoxon rank sum, standard deviations, Fisher, square

Paper

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The authors' code

Java · 266 lines · 31 KB · Apache-2.0 · 1 match

  1. package org.broadinstitute.hellbender.tools.funcotator.mafOutput;
  3. import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation;
  5. import java.util.*;
  6. import java.util.stream.Collectors;
  8. import static org.broadinstitute.hellbender.tools.funcotator.mafOutput.CustomMafFuncotationCreator.MAF_DBSNP_VAL_STATUS_FIELD;
  10. /**
  11. * Class to hold all the constants required for the {@link MafOutputRenderer}.
  12. * Designed to be a simple container class with no methods.
  13. */
  14. public class MafOutputRendererConstants {
  16. //==================================================================================================================
  17. // Static initializers:
  19. static {
  20. final Map<String, String> variantClassMap = new HashMap<>();
  22. variantClassMap.put(GencodeFuncotation.VariantClassification.IN_FRAME_DEL.toString(), "In_Frame_Del");
  23. variantClassMap.put(GencodeFuncotation.VariantClassification.IN_FRAME_INS.toString(), "In_Frame_Ins");
  24. variantClassMap.put(GencodeFuncotation.VariantClassification.FRAME_SHIFT_INS.toString(), "Frame_Shift_Ins");
  25. variantClassMap.put(GencodeFuncotation.VariantClassification.FRAME_SHIFT_DEL.toString(), "Frame_Shift_Del");
  26. variantClassMap.put(GencodeFuncotation.VariantClassification.MISSENSE.toString(), "Missense_Mutation");
  27. variantClassMap.put(GencodeFuncotation.VariantClassification.NONSENSE.toString(), "Nonsense_Mutation");
  28. variantClassMap.put(GencodeFuncotation.VariantClassification.SILENT.toString(), "Silent");
  29. variantClassMap.put(GencodeFuncotation.VariantClassification.SPLICE_SITE.toString(), "Splice_Site");
  30. variantClassMap.put(GencodeFuncotation.VariantClassification.START_CODON_DEL.toString(), "Translation_Start_Site");
  31. variantClassMap.put(GencodeFuncotation.VariantClassification.NONSTOP.toString(), "Nonstop_Mutation");
  32. variantClassMap.put(GencodeFuncotation.VariantClassification.FIVE_PRIME_UTR.toString(), "5'UTR");
  33. variantClassMap.put(GencodeFuncotation.VariantClassification.THREE_PRIME_UTR.toString(), "3'UTR");
  34. variantClassMap.put(GencodeFuncotation.VariantClassification.FIVE_PRIME_FLANK.toString(), "5'Flank");
  35. variantClassMap.put(GencodeFuncotation.VariantClassification.INTRON.toString(), "Intron");
  36. variantClassMap.put(GencodeFuncotation.VariantClassification.LINCRNA.toString(), "RNA");
  38. VariantClassificationMap = variantClassMap;
  39. VariantClassificationMapInverse = variantClassMap.entrySet().stream().collect(Collectors.toMap(Map.Entry::getValue, Map.Entry::getKey));
  40. }
  42. //==================================================================================================================
  43. // High-Level Constants:
  45. /**
  46. * Value to insert into unused annotation columns.
  47. */
  48. static final String UNUSED_STRING = "NA";
  50. /**
  51. * The string representing a comment in a MAF file.
  52. */
  53. static final String COMMENT_STRING = "#";
  55. /**
  56. * Delimiter for fields in the output MAF file.
  57. */
  58. static final String FIELD_DELIMITER = "\t";
  60. /**
  61. * Used for creating funcotations while rendering the MAF.
  62. */
  63. static final String MAF_COUNT_RENDERING_DATASOURCE_DUMMY_NAME = "MAF_COUNT_OUTPUT";
  64. static final String MAF_DBSNP_RENDERING_DATASOURCE_DUMMY_NAME = "MAF_DBSNP_OUTPUT";
  66. //==================================================================================================================
  67. // Specific Field Values:
  69. // Field Names:
  70. public static final String FieldName_Hugo_Symbol = "Hugo_Symbol";
  71. public static final String FieldName_Entrez_Gene_Id = "Entrez_Gene_Id";
  72. public static final String FieldName_Center = "Center";
  73. public static final String FieldName_NCBI_Build = "NCBI_Build";
  74. public static final String FieldName_Chromosome = "Chromosome";
  75. public static final String FieldName_Start_Position = "Start_Position";
  76. public static final String FieldName_End_Position = "End_Position";
  77. public static final String FieldName_Strand = "Strand";
  78. public static final String FieldName_Variant_Classification = "Variant_Classification";
  79. public static final String FieldName_Variant_Type = "Variant_Type";
  80. public static final String FieldName_Reference_Allele = "Reference_Allele";
  81. public static final String FieldName_Tumor_Seq_Allele1 = "Tumor_Seq_Allele1";
  82. public static final String FieldName_Tumor_Seq_Allele2 = "Tumor_Seq_Allele2";
  83. public static final String FieldName_dbSNP_RS = "dbSNP_RS";
  84. public static final String FieldName_dbSNP_Val_Status = "dbSNP_Val_Status";
  85. public static final String FieldName_Tumor_Sample_Barcode = "Tumor_Sample_Barcode";
  86. public static final String FieldName_Matched_Norm_Sample_Barcode = "Matched_Norm_Sample_Barcode";
  87. public static final String FieldName_Match_Norm_Seq_Allele1 = "Match_Norm_Seq_Allele1";
  88. public static final String FieldName_Match_Norm_Seq_Allele2 = "Match_Norm_Seq_Allele2";
  89. public static final String FieldName_Tumor_Validation_Allele1 = "Tumor_Validation_Allele1";
  90. public static final String FieldName_Tumor_Validation_Allele2 = "Tumor_Validation_Allele2";
  91. public static final String FieldName_Match_Norm_Validation_Allele1 = "Match_Norm_Validation_Allele1";
  92. public static final String FieldName_Match_Norm_Validation_Allele2 = "Match_Norm_Validation_Allele2";
  93. public static final String FieldName_Verification_Status = "Verification_Status";
  94. public static final String FieldName_Validation_Status = "Validation_Status";
  95. public static final String FieldName_Mutation_Status = "Mutation_Status";
  96. public static final String FieldName_Sequencing_Phase = "Sequencing_Phase";
  97. public static final String FieldName_Sequence_Source = "Sequence_Source";
  98. public static final String FieldName_Validation_Method = "Validation_Method";
  99. public static final String FieldName_Score = "Score";
  100. public static final String FieldName_BAM_File = "BAM_File";
  101. public static final String FieldName_Sequencer = "Sequencer";
  102. public static final String FieldName_Tumor_Sample_UUID = "Tumor_Sample_UUID";
  103. public static final String FieldName_Matched_Norm_Sample_UUID = "Matched_Norm_Sample_UUID";
  104. public static final String FieldName_Genome_Change = "Genome_Change";
  105. public static final String FieldName_Annotation_Transcript = "Annotation_Transcript";
  106. public static final String FieldName_Transcript_Strand = "Transcript_Strand";
  107. public static final String FieldName_Transcript_Exon = "Transcript_Exon";
  108. public static final String FieldName_Transcript_Position = "Transcript_Position";
  109. public static final String FieldName_cDNA_Change = "cDNA_Change";
  110. public static final String FieldName_Codon_Change = "Codon_Change";
  111. public static final String FieldName_Protein_Change = "Protein_Change";
  112. public static final String FieldName_Other_Transcripts = "Other_Transcripts";
  113. public static final String FieldName_Refseq_mRNA_Id = "Refseq_mRNA_Id";
  114. public static final String FieldName_Refseq_prot_Id = "Refseq_prot_Id";
  115. public static final String FieldName_SwissProt_acc_Id = "SwissProt_acc_Id";
  116. public static final String FieldName_SwissProt_entry_Id = "SwissProt_entry_Id";
  117. public static final String FieldName_Description = "Description";
  118. public static final String FieldName_UniProt_AApos = "UniProt_AApos";
  119. public static final String FieldName_UniProt_Region = "UniProt_Region";
  120. public static final String FieldName_UniProt_Site = "UniProt_Site";
  121. public static final String FieldName_UniProt_Natural_Variations = "UniProt_Natural_Variations";
  122. public static final String FieldName_UniProt_Experimental_Info = "UniProt_Experimental_Info";
  123. public static final String FieldName_GO_Biological_Process = "GO_Biological_Process";
  124. public static final String FieldName_GO_Cellular_Component = "GO_Cellular_Component";
  125. public static final String FieldName_GO_Molecular_Function = "GO_Molecular_Function";
  126. public static final String FieldName_COSMIC_overlapping_mutations = "COSMIC_overlapping_mutations";
  127. public static final String FieldName_COSMIC_fusion_genes = "COSMIC_fusion_genes";
  128. public static final String FieldName_COSMIC_tissue_types_affected = "COSMIC_tissue_types_affected";
  129. public static final String FieldName_COSMIC_total_alterations_in_gene = "COSMIC_total_alterations_in_gene";
  130. public static final String FieldName_Tumorscape_Amplification_Peaks = "Tumorscape_Amplification_Peaks";
  131. public static final String FieldName_Tumorscape_Deletion_Peaks = "Tumorscape_Deletion_Peaks";
  132. public static final String FieldName_TCGAscape_Amplification_Peaks = "TCGAscape_Amplification_Peaks";
  133. public static final String FieldName_TCGAscape_Deletion_Peaks = "TCGAscape_Deletion_Peaks";
  134. public static final String FieldName_DrugBank = "DrugBank";
  135. public static final String FieldName_ref_context = "ref_context";
  136. public static final String FieldName_gc_content = "gc_content";
  137. public static final String FieldName_CCLE_ONCOMAP_overlapping_mutations = "CCLE_ONCOMAP_overlapping_mutations";
  138. public static final String FieldName_CCLE_ONCOMAP_total_mutations_in_gene = "CCLE_ONCOMAP_total_mutations_in_gene";
  139. public static final String FieldName_CGC_Mutation_Type = "CGC_Mutation_Type";
  140. public static final String FieldName_CGC_Translocation_Partner = "CGC_Translocation_Partner";
  141. public static final String FieldName_CGC_Tumor_Types_Somatic = "CGC_Tumor_Types_Somatic";
  142. public static final String FieldName_CGC_Tumor_Types_Germline = "CGC_Tumor_Types_Germline";
  143. public static final String FieldName_CGC_Other_Diseases = "CGC_Other_Diseases";
  144. public static final String FieldName_DNARepairGenes_Activity_linked_to_OMIM = "DNARepairGenes_Activity_linked_to_OMIM";
  145. public static final String FieldName_FamilialCancerDatabase_Syndromes = "FamilialCancerDatabase_Syndromes";
  146. public static final String FieldName_MUTSIG_Published_Results = "MUTSIG_Published_Results";
  147. public static final String FieldName_OREGANNO_ID = "OREGANNO_ID";
  148. public static final String FieldName_OREGANNO_Values = "OREGANNO_Values";
  149. public static final String FieldName_tumor_f = "tumor_f";
  150. public static final String FieldName_t_alt_count = "t_alt_count";
  151. public static final String FieldName_t_ref_count = "t_ref_count";
  152. public static final String FieldName_n_alt_count = "n_alt_count";
  153. public static final String FieldName_n_ref_count = "n_ref_count";
  156. // db SNP specific
  157. /**
  158. * The funcotation factory name that must be specified in the config for the custom MAF renderer to recognize it as a dbSNP annotation.
  159. */
  160. static final String DBSNP_DS_NAME = "dbSNP";
  162. /**
  163. * The funcotation factory result we should expect for the dbsnp validation flag.
  164. */
  165. static final String DBSNP_VLD_NAME = DBSNP_DS_NAME + "_VLD";
  167. // Field Values:
  168. static final String FieldValue_Strand = "+";
  169. static final String OTHER_TRANSCRIPT_DELIMITER = "|";
  170. static final String FieldValue_Variant_Type_Insertion = "INS";
  171. static final String FieldValue_Variant_Type_Deletion = "DEL";
  172. static final String FieldValue_Gencode_Chromosome_Mito = "chrM";
  173. static final String FieldValue_Chromosome_Mito = "MT";
  174. static final String EmptyAllele = "-";
  176. // Variant Classification Map:
  177. static final Map<String, String> VariantClassificationMap;
  178. static final Map<String, String> VariantClassificationMapInverse;
  180. // Output Field Name Map Defaults:
  181. //TODO these are hardcoded to gencode versions and should be updated to generalize to any version of gencode (see https://github.com/broadinstitute/gatk/issues/8482)
  182. static final List<String> OutputFieldNameMap_Hugo_Symbol = Arrays.asList(FieldName_Hugo_Symbol, "Gencode_19_hugoSymbol", "Gencode_27_hugoSymbol", "Gencode_28_hugoSymbol", "Gencode_34_hugoSymbol", "Gencode_43_hugoSymbol", "gene", "Gene");
  183. static final List<String> OutputFieldNameMap_Entrez_Gene_Id = Arrays.asList(FieldName_Entrez_Gene_Id, "HGNC_Entrez_Gene_ID", "HGNC_Entrez Gene ID", "HGNC_Entrez_Gene_ID(supplied_by_NCBI)", "HGNC_Entrez Gene ID(supplied by NCBI)", "entrez_id", "gene_id");
  184. static final List<String> OutputFieldNameMap_Center = Arrays.asList(FieldName_Center, "center");
  185. static final List<String> OutputFieldNameMap_NCBI_Build = Arrays.asList(FieldName_NCBI_Build, "Gencode_19_ncbiBuild", "Gencode_27_ncbiBuild", "Gencode_28_ncbiBuild", "Gencode_34_ncbiBuild", "Gencode_43_ncbiBuild", "ncbi_build");
  186. static final List<String> OutputFieldNameMap_Chromosome = Arrays.asList(FieldName_Chromosome, "Gencode_19_chromosome", "Gencode_27_chromosome", "Gencode_28_chromosome", "Gencode_34_chromosome", "Gencode_43_chromosome", "chr", "contig", "chromosome", "chrom", "Chrom");
  187. static final List<String> OutputFieldNameMap_Start_Position = Arrays.asList(FieldName_Start_Position, "Start_position", "Gencode_19_start", "Gencode_27_start", "Gencode_28_start", "Gencode_34_start", "Gencode_43_start", "start", "Start", "start_pos", "pos");
  188. static final List<String> OutputFieldNameMap_End_Position = Arrays.asList(FieldName_End_Position, "End_position", "Gencode_19_end", "Gencode_27_end", "Gencode_28_end", "Gencode_34_end", "Gencode_43_end", "end", "End", "end_pos");
  189. static final List<String> OutputFieldNameMap_Strand = Collections.singletonList(FieldName_Strand);
  190. static final List<String> OutputFieldNameMap_Variant_Classification = Arrays.asList(FieldName_Variant_Classification, "Gencode_19_variantClassification", "Gencode_27_variantClassification", "Gencode_28_variantClassification", "Gencode_34_variantClassification", "Gencode_43_variantClassification", "variant_classification");
  191. static final List<String> OutputFieldNameMap_Variant_Type = Arrays.asList(FieldName_Variant_Type, "Gencode_19_variantType", "Gencode_27_variantType", "Gencode_28_variantType", "Gencode_34_variantType", "Gencode_43_variantType", "variant_type");
  192. static final List<String> OutputFieldNameMap_Reference_Allele = Arrays.asList(FieldName_Reference_Allele, "Gencode_19_refAllele", "Gencode_27_refAllele", "Gencode_28_refAllele", "Gencode_34_refAllele", "Gencode_43_refAllele", "ref", "ref_allele", "reference_allele");
  193. static final List<String> OutputFieldNameMap_Tumor_Seq_Allele1 = Arrays.asList(FieldName_Tumor_Seq_Allele1, "Gencode_19_tumorSeqAllele1", "Gencode_27_tumorSeqAllele1", "Gencode_28_tumorSeqAllele1", "Gencode_34_tumorSeqAllele1", "Gencode_43_tumorSeqAllele1", "ref", "ref_allele", "reference_allele");
  194. static final List<String> OutputFieldNameMap_Tumor_Seq_Allele2 = Arrays.asList(FieldName_Tumor_Seq_Allele2, "Gencode_19_tumorSeqAllele2", "Gencode_27_tumorSeqAllele2", "Gencode_28_tumorSeqAllele2", "Gencode_34_tumorSeqAllele2", "Gencode_43_tumorSeqAllele2", "alt", "alt_allele", "alt2", "alt_allele2", "alternate_allele2", "observed_allele2", "alternate_allele", "observed_allele", "alt1", "alt_allele1", "alternate_allele1", "observed_allele1");
  195. static final List<String> OutputFieldNameMap_dbSNP_RS = Arrays.asList(FieldName_dbSNP_RS, "dbsnp_rs", "dbSNP_RSPOS");
  196. static final List<String> OutputFieldNameMap_dbSNP_Val_Status = Arrays.asList(FieldName_dbSNP_Val_Status, MAF_DBSNP_VAL_STATUS_FIELD, "dbsnp_val_status", DBSNP_VLD_NAME);
  197. static final List<String> OutputFieldNameMap_Tumor_Sample_Barcode = Arrays.asList(FieldName_Tumor_Sample_Barcode, "tumor_barcode", "tumor_id", "case_barcode", "case_id", "tumor_name");
  198. static final List<String> OutputFieldNameMap_Matched_Norm_Sample_Barcode = Arrays.asList(FieldName_Matched_Norm_Sample_Barcode, "normal_barcode", "normal_id", "control_barcode", "control_id", "normal_name", "sample_name");
  199. static final List<String> OutputFieldNameMap_Match_Norm_Seq_Allele1 = Arrays.asList(FieldName_Match_Norm_Seq_Allele1, "Match_Norm_Seq_Allele1");
  200. static final List<String> OutputFieldNameMap_Match_Norm_Seq_Allele2 = Arrays.asList(FieldName_Match_Norm_Seq_Allele2, "Match_Norm_Seq_Allele2");
  201. static final List<String> OutputFieldNameMap_Tumor_Validation_Allele1 = Arrays.asList(FieldName_Tumor_Validation_Allele1, "Tumor_Validation_Allele1");
  202. static final List<String> OutputFieldNameMap_Tumor_Validation_Allele2 = Arrays.asList(FieldName_Tumor_Validation_Allele2, "Tumor_Validation_Allele2");
  203. static final List<String> OutputFieldNameMap_Match_Norm_Validation_Allele1 = Arrays.asList(FieldName_Match_Norm_Validation_Allele1, "Match_Norm_Validation_Allele1");
  204. static final List<String> OutputFieldNameMap_Match_Norm_Validation_Allele2 = Arrays.asList(FieldName_Match_Norm_Validation_Allele2, "Match_Norm_Validation_Allele2");
  205. static final List<String> OutputFieldNameMap_Verification_Status = Arrays.asList(FieldName_Verification_Status, "Verification_Status");
  206. static final List<String> OutputFieldNameMap_Validation_Status = Arrays.asList(FieldName_Validation_Status, "validation_status");
  207. static final List<String> OutputFieldNameMap_Mutation_Status = Arrays.asList(FieldName_Mutation_Status, "status");
  208. static final List<String> OutputFieldNameMap_Sequencing_Phase = Arrays.asList(FieldName_Sequencing_Phase, "phase");
  209. static final List<String> OutputFieldNameMap_Sequence_Source = Arrays.asList(FieldName_Sequence_Source, "source");
  210. static final List<String> OutputFieldNameMap_Validation_Method = Arrays.asList(FieldName_Validation_Method, "Validation_Method");
  211. static final List<String> OutputFieldNameMap_Score = Arrays.asList(FieldName_Score, "Score");
  212. static final List<String> OutputFieldNameMap_BAM_File = Arrays.asList(FieldName_BAM_File, "BAM_file", "bam", "bam_file");
  213. static final List<String> OutputFieldNameMap_Sequencer = Arrays.asList(FieldName_Sequencer, "sequencer", "platform");
  214. static final List<String> OutputFieldNameMap_Tumor_Sample_UUID = Arrays.asList(FieldName_Tumor_Sample_UUID, "tumor_uuid", "case_uuid", "tumor_barcode", "tumor_id", "case_barcode", "case_id", "tumor_name", "Tumor_Sample_Barcode");
  215. static final List<String> OutputFieldNameMap_Matched_Norm_Sample_UUID = Arrays.asList(FieldName_Matched_Norm_Sample_UUID, "normal_uuid", "control_uuid", "normal_barcode", "normal_id", "control_barcode", "control_id", "normal_name", "sample_name", "Matched_Norm_Sample_Barcode");
  216. static final List<String> OutputFieldNameMap_Genome_Change = Arrays.asList(FieldName_Genome_Change, "Gencode_19_genomeChange", "Gencode_27_genomeChange", "Gencode_28_genomeChange", "Gencode_34_genomeChange", "Gencode_43_genomeChange", "genome_change");
  217. static final List<String> OutputFieldNameMap_Annotation_Transcript = Arrays.asList(FieldName_Annotation_Transcript, "Gencode_19_annotationTranscript", "Gencode_27_annotationTranscript", "Gencode_28_annotationTranscript", "Gencode_34_annotationTranscript", "Gencode_43_annotationTranscript", "annotation_transcript", "transcript_id");
  218. static final List<String> OutputFieldNameMap_Transcript_Strand = Arrays.asList(FieldName_Transcript_Strand, "Gencode_19_transcriptStrand", "Gencode_27_transcriptStrand", "Gencode_28_transcriptStrand", "Gencode_34_transcriptStrand", "Gencode_43_transcriptStrand", "transcript_strand");
  219. static final List<String> OutputFieldNameMap_Transcript_Exon = Arrays.asList(FieldName_Transcript_Exon, "Gencode_19_transcriptExon", "Gencode_27_transcriptExon", "Gencode_28_transcriptExon", "Gencode_34_transcriptExon", "Gencode_43_transcriptExon", "transcript_exon");
  220. static final List<String> OutputFieldNameMap_Transcript_Position = Arrays.asList(FieldName_Transcript_Position, "Gencode_19_transcriptPos", "Gencode_27_transcriptPos", "Gencode_28_transcriptPos", "Gencode_34_transcriptPos", "Gencode_43_transcriptPos", "transcript_position");
  221. static final List<String> OutputFieldNameMap_cDNA_Change = Arrays.asList(FieldName_cDNA_Change, "Gencode_19_cDnaChange", "Gencode_27_cDnaChange", "Gencode_28_cDnaChange", "Gencode_34_cDnaChange", "Gencode_43_cDnaChange", "transcript_change");
  222. static final List<String> OutputFieldNameMap_Codon_Change = Arrays.asList(FieldName_Codon_Change, "Gencode_19_codonChange", "Gencode_27_codonChange", "Gencode_28_codonChange", "Gencode_34_codonChange", "Gencode_43_codonChange", "codon_change");
  223. static final List<String> OutputFieldNameMap_Protein_Change = Arrays.asList(FieldName_Protein_Change, "Gencode_19_proteinChange", "Gencode_27_proteinChange", "Gencode_28_proteinChange", "Gencode_34_proteinChange", "Gencode_43_proteinChange", "protein_change");
  224. static final List<String> OutputFieldNameMap_Other_Transcripts = Arrays.asList(FieldName_Other_Transcripts, "Gencode_19_otherTranscripts", "Gencode_27_otherTranscripts", "Gencode_28_otherTranscripts", "Gencode_34_otherTranscripts", "Gencode_43_otherTranscripts", "other_transcripts");
  225. static final List<String> OutputFieldNameMap_Refseq_mRNA_Id = Arrays.asList(FieldName_Refseq_mRNA_Id, "Gencode_XRefSeq_mRNA_id", "gencode_xref_refseq_mRNA_id", "ENSEMBL_RefSeq_mRNA_accession", "RefSeq_mRNA_Id", "HGNC_RefSeq IDs");
  226. static final List<String> OutputFieldNameMap_Refseq_prot_Id = Arrays.asList(FieldName_Refseq_prot_Id, "Gencode_XRefSeq_prot_acc", "gencode_xref_refseq_prot_acc", "ENSEMBL_RefSeq_protein_accession", "RefSeq_prot_Id");
  227. static final List<String> OutputFieldNameMap_SwissProt_acc_Id = Arrays.asList(FieldName_SwissProt_acc_Id, "Simple_Uniprot_uniprot_accession", "uniprot_accession", "UniProt_uniprot_accession");
  228. static final List<String> OutputFieldNameMap_SwissProt_entry_Id = Arrays.asList(FieldName_SwissProt_entry_Id, "Simple_Uniprot_uniprot_entry_name", "uniprot_entry_name", "UniProt_uniprot_entry_name");
  229. static final List<String> OutputFieldNameMap_Description = Arrays.asList(FieldName_Description, "RefSeq_Description", "HGNC_Approved_Name", "HGNC_Approved Name");
  230. static final List<String> OutputFieldNameMap_UniProt_AApos = Arrays.asList(FieldName_UniProt_AApos, "UniProt_AAxform_aapos", "uniprot_AA_pos");
  231. static final List<String> OutputFieldNameMap_UniProt_Region = Arrays.asList(FieldName_UniProt_Region, "UniProt_AA_region");
  232. static final List<String> OutputFieldNameMap_UniProt_Site = Arrays.asList(FieldName_UniProt_Site, "UniProt_AA_site");
  233. static final List<String> OutputFieldNameMap_UniProt_Natural_Variations = Arrays.asList(FieldName_UniProt_Natural_Variations, "UniProt_AA_natural_variation");
  234. static final List<String> OutputFieldNameMap_UniProt_Experimental_Info = Arrays.asList(FieldName_UniProt_Experimental_Info, "UniProt_AA_experimental_info");
  235. static final List<String> OutputFieldNameMap_GO_Biological_Process = Arrays.asList(FieldName_GO_Biological_Process, "Simple_Uniprot_GO_Biological_Process", "UniProt_GO_Biological_Process");
  236. static final List<String> OutputFieldNameMap_GO_Cellular_Component = Arrays.asList(FieldName_GO_Cellular_Component, "Simple_Uniprot_GO_Cellular_Component", "UniProt_GO_Cellular_Component");
  237. static final List<String> OutputFieldNameMap_GO_Molecular_Function = Arrays.asList(FieldName_GO_Molecular_Function, "Simple_Uniprot_GO_Molecular_Function", "UniProt_GO_Molecular_Function");
  238. static final List<String> OutputFieldNameMap_COSMIC_overlapping_mutations = Arrays.asList(FieldName_COSMIC_overlapping_mutations, "Cosmic_overlapping_mutations", "COSMIC_overlapping_mutations", "COSMIC_overlapping_mutation_AAs");
  239. static final List<String> OutputFieldNameMap_COSMIC_fusion_genes = Arrays.asList(FieldName_COSMIC_fusion_genes, "CosmicFusion_fusion_genes", "COSMIC_FusionGenes_fusion_genes");
  240. static final List<String> OutputFieldNameMap_COSMIC_tissue_types_affected = Arrays.asList(FieldName_COSMIC_tissue_types_affected, "CosmicTissue_tissue_types_affected", "COSMIC_tissue_types_affected", "COSMIC_Tissue_tissue_types_affected");
  241. static final List<String> OutputFieldNameMap_COSMIC_total_alterations_in_gene = Arrays.asList(FieldName_COSMIC_total_alterations_in_gene, "CosmicTissue_total_alterations_in_gene", "COSMIC_total_alterations_in_gene", "COSMIC_Tissue_total_alterations_in_gene");
  242. static final List<String> OutputFieldNameMap_Tumorscape_Amplification_Peaks = Arrays.asList(FieldName_Tumorscape_Amplification_Peaks, "TUMORScape_Amplification_Peaks");
  243. static final List<String> OutputFieldNameMap_Tumorscape_Deletion_Peaks = Arrays.asList(FieldName_Tumorscape_Deletion_Peaks, "TUMORScape_Deletion_Peaks");
  244. static final List<String> OutputFieldNameMap_TCGAscape_Amplification_Peaks = Arrays.asList(FieldName_TCGAscape_Amplification_Peaks, "TCGAScape_Amplification_Peaks");
  245. static final List<String> OutputFieldNameMap_TCGAscape_Deletion_Peaks = Arrays.asList(FieldName_TCGAscape_Deletion_Peaks, "TCGAScape_Deletion_Peaks");
  246. static final List<String> OutputFieldNameMap_DrugBank = Arrays.asList(FieldName_DrugBank, "Simple_Uniprot_DrugBank", "UniProt_DrugBank");
  247. static final List<String> OutputFieldNameMap_ref_context = Arrays.asList(FieldName_ref_context, "Gencode_19_referenceContext", "Gencode_27_referenceContext", "Gencode_28_referenceContext", "Gencode_34_referenceContext", "Gencode_43_referenceContext", "ref_context");
  248. static final List<String> OutputFieldNameMap_gc_content = Arrays.asList(FieldName_gc_content, "Gencode_19_gcContent", "Gencode_27_gcContent", "Gencode_28_gcContent", "Gencode_34_gcContent", "Gencode_43_gcContent", "gc_content");
  249. static final List<String> OutputFieldNameMap_CCLE_ONCOMAP_overlapping_mutations = Arrays.asList(FieldName_CCLE_ONCOMAP_overlapping_mutations, "CCLE_By_GP_overlapping_mutations");
  250. static final List<String> OutputFieldNameMap_CCLE_ONCOMAP_total_mutations_in_gene = Arrays.asList(FieldName_CCLE_ONCOMAP_total_mutations_in_gene, "CCLE_By_Gene_total_mutations_in_gene");
  251. static final List<String> OutputFieldNameMap_CGC_Mutation_Type = Arrays.asList(FieldName_CGC_Mutation_Type, "CGC_Mutation Type");
  252. static final List<String> OutputFieldNameMap_CGC_Translocation_Partner = Arrays.asList(FieldName_CGC_Translocation_Partner, "CGC_Translocation Partner");
  253. static final List<String> OutputFieldNameMap_CGC_Tumor_Types_Somatic = Arrays.asList(FieldName_CGC_Tumor_Types_Somatic, "CGC_Tumour Types (Somatic Mutations)", "CGC_Tumour_Types__(Somatic_Mutations)");
  254. static final List<String> OutputFieldNameMap_CGC_Tumor_Types_Germline = Arrays.asList(FieldName_CGC_Tumor_Types_Germline, "CGC_Tumour Types (Germline Mutations)", "CGC_Tumour_Types_(Germline_Mutations)");
  255. static final List<String> OutputFieldNameMap_CGC_Other_Diseases = Arrays.asList(FieldName_CGC_Other_Diseases, "CGC_Other Syndrome/Disease", "CGC_Other_Syndrome/Disease");
  256. static final List<String> OutputFieldNameMap_DNARepairGenes_Activity_linked_to_OMIM = Collections.singletonList(FieldName_DNARepairGenes_Activity_linked_to_OMIM);
  257. static final List<String> OutputFieldNameMap_FamilialCancerDatabase_Syndromes = Arrays.asList(FieldName_FamilialCancerDatabase_Syndromes, "Familial_Cancer_Genes_Syndrome");
  258. static final List<String> OutputFieldNameMap_MUTSIG_Published_Results = Arrays.asList(FieldName_MUTSIG_Published_Results, "MutSig Published Results_Published_Results");
  259. static final List<String> OutputFieldNameMap_OREGANNO_ID = Arrays.asList(FieldName_OREGANNO_ID, "Oreganno_ID", "ORegAnno_ID");
  260. static final List<String> OutputFieldNameMap_OREGANNO_Values = Arrays.asList(FieldName_OREGANNO_Values, "Oreganno_Values", "ORegAnno_Values");
  261. static final List<String> OutputFieldNameMap_tumor_f = Arrays.asList(FieldName_tumor_f, "sample_allelic_fraction");
  262. static final List<String> OutputFieldNameMap_t_alt_count = Collections.singletonList(FieldName_t_alt_count);
  263. static final List<String> OutputFieldNameMap_t_ref_count = Collections.singletonList(FieldName_t_ref_count);
  264. static final List<String> OutputFieldNameMap_n_alt_count = Collections.singletonList(FieldName_n_alt_count);
  265. static final List<String> OutputFieldNameMap_n_ref_count = Collections.singletonList(FieldName_n_ref_count);
  266. }

MafOutputRendererConstants.java at commit 0cde69e, under Apache-2.0 · at the source

Overview

Authors: Huan Yan1,2,3, Wenjuan Jiang2, Yi Xiong2, Li Liu2, Renzhi Zhang1,2,4, Zhaohui Ruan1,5, Zhe Huang1,6, Jiacheng Dai1,2, Fang Tian1,2,3, Chunhua Zhou2, Zhan Wang2, Haiyan Yang2, Wei Tao7, Hongbo Zheng7, Qinqin Xu3,8, Nong Yang9, Liang Zeng1,2, Yongchang Zhang1,2,3,4,5,6
ORCID iDs: Yongchang Zhang
  1. Early Clinical Trial Center, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
  2. Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
  3. College of Clinical Medicine, Qinghai University, Xining 810000, Qinghai, China
  4. Graduate Collaborative Training Base of Hunan Cancer Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
  5. Third Xiangya Hospital, Central South University, Changsha 410000, China
  6. School of Basic Medicine Sciences, Central South University, Changsha 410078, Hunan, China
  7. Genecast Biotechnology Co., Ltd. Wuxi, Wuxi 214000, China
  8. Department of Medical Oncology, Qinghai Provincial People’s Hospital, Xining 810000, China
  9. Hunan Provincial Second People’s Hospital, Changsha 410013, Hunan, China
Institutions: Qinghai University (China); Central South University (China); Hunan Cancer Hospital (China); University of South China (China); Third Xiangya Hospital (China); Qinghai Provincial Peoples Hospital (China); Second People Hospital of Hunan (China)
Journal: Cell reports. Medicine, volume 7, issue 7, article 102904
Dates: received 21 October 2025; accepted 8 June 2026; published online 30 June 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.xcrm.2026.102904 · PMID 42379171 · PMCID PMC13400170 · OpenAlex W7166646818
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), other condition (population)
Methods: Statistics, Preprocessing
Keywords: furmonertinib, non-small cell lung cancer, EGFR mutation, central nervous system metastases, third-generation EGFR-TKI
MeSH: Antineoplastic Agents*, Carcinoma, Non-Small-Cell Lung*, Central Nervous System Neoplasms*, Lung Neoplasms*, Mutation*, Adult, Aged, Brain Neoplasms, ErbB Receptors, Female, Humans, Male, Middle Aged, Protein Kinase Inhibitors (* major topic)
Topic: Lung Cancer Treatments and Mutations (Pulmonary and Respiratory Medicine, Medicine), according to OpenAlex
Funding: National Natural Science Foundation of China; Chongqing Municipality Key Research and Development Program of China
Citations: not cited yet (Europe PMC); 42 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

broadinstitute/gatk

License: Apache-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 0cde69eed30339f5978cbb1ac6e5cf3662f9e1f8, 17 August 2026
Languages: Java (2500), Python (88), Shell (72), R (11), Jupyter (1), JavaScript (1)
Size: 7,086 files, 2,673 scripts
Software Heritage: archived
Found in: the resources table
Holds: README, license file, environment (Dockerfile, scripts/docker/gatkbase/Dockerfile, scripts/mitochondria_m2_wdl/Haplochecker/Dockerfile, src/main/python/org/broadinstitute/hellbender/setup.py), tests, continuous integration, documentation, 1 notebook
Not found: CITATION.cff
Tools: NumPy (36 files), PyMC (15 files), PyTorch (8 files), pysam (4 files), ggplot2 (3 files), SAMtools (3 files), SciPy (3 files), Biopython (2 files), data.table (2 files), h5py (2 files), PyTorch Lightning (2 files), pandas (2 files), tidyverse (2 files), scikit-learn (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
2,000 files
At the source: github.com/broadinstitute/gatk/releases

The paper's code and data availability statement is in the Data section.

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1,998 scripts, each with its path and the digest of its content;
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Data

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Code and data availability statement

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Read it in the paper: doi.org/10.1016/j.xcrm.2026.102904.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

  • Authors: added Yongchang Zhang (0000-0002-6829-7176); removed Yongchang Zhang

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 18 authors, 5 keywords, 14 MeSH terms, 2 funders, 41 references.

Cite

This paper

Yan, H., Jiang, W., Xiong, Y., Liu, L., Zhang, R., Ruan, Z., Huang, Z., Dai, J., Tian, F., Zhou, C., Wang, Z., Yang, H., Tao, W., Zheng, H., Xu, Q., Yang, N., Zeng, L., & Zhang, Y. (2026). High-dose furmonertinib as first-line treatment for untreated EGFR-mutated advanced NSCLC with central nervous system metastases: A phase 2 trial. Cell reports. Medicine, 7(7), 102904. https://doi.org/10.1016/j.xcrm.2026.102904

BibTeX

@article{yan2026high,
author = {Yan, Huan and Jiang, Wenjuan and Xiong, Yi and Liu, Li and Zhang, Renzhi and Ruan, Zhaohui and Huang, Zhe and Dai, Jiacheng and Tian, Fang and Zhou, Chunhua and Wang, Zhan and Yang, Haiyan and Tao, Wei and Zheng, Hongbo and Xu, Qinqin and Yang, Nong and Zeng, Liang and Zhang, Yongchang},
title = {{High-dose furmonertinib as first-line treatment for untreated EGFR-mutated advanced NSCLC with central nervous system metastases: A phase 2 trial}},
journal = {Cell reports. Medicine},
year = {2026},
month = jun,
volume = {7},
number = {7},
pages = {102904},
publisher = {Elsevier},
issn = {2666-3791},
doi = {10.1016/j.xcrm.2026.102904},
url = {https://doi.org/10.1016/j.xcrm.2026.102904},
pmid = {42379171},
pmcid = {PMC13400170}
}

RIS

TY - JOUR
AU - Yan, Huan
AU - Jiang, Wenjuan
AU - Xiong, Yi
AU - Liu, Li
AU - Zhang, Renzhi
AU - Ruan, Zhaohui
AU - Huang, Zhe
AU - Dai, Jiacheng
AU - Tian, Fang
AU - Zhou, Chunhua
AU - Wang, Zhan
AU - Yang, Haiyan
AU - Tao, Wei
AU - Zheng, Hongbo
AU - Xu, Qinqin
AU - Yang, Nong
AU - Zeng, Liang
AU - Zhang, Yongchang
TI - High-dose furmonertinib as first-line treatment for untreated EGFR-mutated advanced NSCLC with central nervous system metastases: A phase 2 trial
T2 - Cell reports. Medicine
J2 - Cell Rep Med
PY - 2026
DA - 2026/06/30
VL - 7
IS - 7
SP - 102904
SN - 2666-3791
PB - Elsevier
DO - 10.1016/j.xcrm.2026.102904
UR - https://doi.org/10.1016/j.xcrm.2026.102904
LA - en
ER -

CSL-JSON

{
"id": "10.1016/j.xcrm.2026.102904",
"type": "article-journal",
"title": "High-dose furmonertinib as first-line treatment for untreated EGFR-mutated advanced NSCLC with central nervous system metastases: A phase 2 trial",
"container-title": "Cell reports. Medicine",
"author": [
{
"family": "Yan",
"given": "Huan"
},
{
"family": "Jiang",
"given": "Wenjuan"
},
{
"family": "Xiong",
"given": "Yi"
},
{
"family": "Liu",
"given": "Li"
},
{
"family": "Zhang",
"given": "Renzhi"
},
{
"family": "Ruan",
"given": "Zhaohui"
},
{
"family": "Huang",
"given": "Zhe"
},
{
"family": "Dai",
"given": "Jiacheng"
},
{
"family": "Tian",
"given": "Fang"
},
{
"family": "Zhou",
"given": "Chunhua"
},
{
"family": "Wang",
"given": "Zhan"
},
{
"family": "Yang",
"given": "Haiyan"
},
{
"family": "Tao",
"given": "Wei"
},
{
"family": "Zheng",
"given": "Hongbo"
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{
"family": "Xu",
"given": "Qinqin"
},
{
"family": "Yang",
"given": "Nong"
},
{
"family": "Zeng",
"given": "Liang"
},
{
"family": "Zhang",
"given": "Yongchang"
}
],
"container-title-short": "Cell Rep Med",
"volume": "7",
"issue": "7",
"page": "102904",
"DOI": "10.1016/j.xcrm.2026.102904",
"PMID": "42379171",
"PMCID": "PMC13400170",
"ISSN": "2666-3791",
"publisher": "Elsevier",
"URL": "https://doi.org/10.1016/j.xcrm.2026.102904",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
30
]
]
}
}

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