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Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes.

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  1. [1] § Materials and methods › HLA typing, mutation detection ↔ src/FunctionalTester.py, lines 214–234 · score 0.61 · Mutation pipeline, reference genome, Variant Call, STAR, bam, VCF

Paper

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The authors' code

Python · 372 lines · 18 KB · BSD-3-Clause · 1 match

  1. __author__ = "Timothy Tickle"
  2. __copyright__ = "Copyright 2015"
  3. __credits__ = ["Timothy Tickle", "Brian Haas"]
  4. __license__ = "MIT"
  5. __maintainer__ = "Timothy Tickle"
  6. __email__ = "[email hidden]"
  7. __status__ = "Development"
  8. import Commandline
  9. import os
  10. import ParentPipelineTester
  11. import unittest
  12. class FunctionalTester(ParentPipelineTester.ParentPipelineTester):
  13. """
  14. Functional testing for scripts, these are focused on making sure the script can be called in different ways and complete without error.
  15. """
  16. # Testing environment
  17. str_script_dir = "/ahg/regev/users/ttickle/dev/Trinity_CTAT/mutation/src"
  18. str_test_data = "/seq/RNASEQ/public_ftp/CTAT/mutation/demo_data"
  19. str_testing_area = "/broad/hptmp/ttickle/active_testing_script_tester"
  20. os.environ['PATH'] = ":".join([str_script_dir,os.getenv('PATH',None)])
  21. str_input_index = os.path.join(str_test_data, "Hg19_11")
  22. str_input_test_bam = os.path.join(str_test_data, "Aligned.sortedByCoord.out.bam")
  23. str_left_file = os.path.join(str_test_data, "FLI1.left.fq")
  24. str_right_file = os.path.join(str_test_data, "FLI1.right.fq")
  25. str_reference_vcf = os.path.join(str_test_data, "dbsnp_FLI1.vcf")
  26. str_reference_genome = os.path.join(str_test_data, "Hg19_11.fa")
  27. str_update_command = "".join(["--update AddOrReplaceReadGroups.jar",
  28. ":/seq/regev_genome_portal/SOFTWARE/Picard/current,",
  29. "MarkDuplicates.jar",
  30. ":/seq/regev_genome_portal/SOFTWARE/Picard/current,",
  31. "SortSam.jar",
  32. ":/seq/regev_genome_portal/SOFTWARE/Picard/current,",
  33. "snpEff.jar",
  34. ":/seq/regev_genome_portal/SOFTWARE/snpEff,",
  35. "GenomeAnalysisTK.jar",
  36. ":/humgen/gsa-hpprojects/GATK/bin/GenomeAnalysisTK-3.1-1-g07a4bf8"])
  37. def test_rnaseq_mutation_pipeline_for_no_args(self):
  38. """
  39. Tests rnaseq_mutation_pipeline.py for no args call.
  40. """
  41. # Create test environment
  42. str_command = "python rnaseq_mutation_pipeline.py"
  43. # Run command
  44. f_success = Commandline.Commandline().func_CMD(str_command)
  45. # Test error
  46. self.assertFalse(f_success, str_command)
  47. def test_rnaseq_mutation_pipeline_for_args_short(self):
  48. """
  49. Tests rnaseq_mutation_pipeline.py for help args call short.
  50. """
  51. # Create test environment
  52. str_command = "python rnaseq_mutation_pipeline.py -h"
  53. # Run command
  54. f_success = Commandline.Commandline().func_CMD(str_command)
  55. # Test error
  56. self.assertTrue(f_success, str_command)
  57. def test_rnaseq_mutation_pipeline_for_args_long(self):
  58. """
  59. Tests rnaseq_mutation_pipeline.py for help args call short.
  60. """
  61. # Create test environment
  62. str_command = "python rnaseq_mutation_pipeline.py --help"
  63. # Run command
  64. f_success = Commandline.Commandline().func_CMD(str_command)
  65. # Test error
  66. self.assertTrue(f_success, str_command)
  67. def test_rnaseq_mutation_pipeline_for_test(self):
  68. """
  69. Tests rnaseq_mutation_pipeline.py for test mode.
  70. """
  71. # Create test environment
  72. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  73. "--alignment_mode STAR",
  74. "--variant_call_mode GATK",
  75. "--threads 8",
  76. "--plot",
  77. "--reference", self.str_reference_genome,
  78. "--left", self.str_left_file,
  79. "--right", self.str_right_file,
  80. "--test",
  81. "--out_dir", "_".join([self.str_testing_area,"vanilla_test"]),
  82. "--vcf",self.str_reference_vcf,
  83. self.str_update_command])
  84. # Run command
  85. f_success = Commandline.Commandline().func_CMD(str_command)
  86. # Test error
  87. self.assertTrue(f_success, str_command)
  88. def test_rnaseq_mutation_pipeline_for_gatk_call(self):
  89. """
  90. Tests rnaseq_mutation_pipeline.py for gatk call.
  91. """
  92. str_output_dir = os.path.join(self.str_testing_area,"vanilla_gatk")
  93. self.func_make_dummy_dirs([self.str_testing_area, str_output_dir])
  94. # Create test environment
  95. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  96. "--alignment_mode STAR",
  97. "--variant_call_mode GATK",
  98. "--threads 8",
  99. "--plot",
  100. "--reference", self.str_reference_genome,
  101. "--left", self.str_left_file,
  102. "--right", self.str_right_file,
  103. "--variant_filtering_mode GATK",
  104. "--out_dir",
  105. str_output_dir,
  106. "--vcf", self.str_reference_vcf,
  107. self.str_update_command])
  108. # Run command
  109. f_success = Commandline.Commandline().func_CMD(str_command)
  110. # Test error
  111. self.assertTrue(f_success, str_command)
  112. def test_rnaseq_mutation_pipeline_for_compression(self):
  113. """
  114. Tests rnaseq_mutation_pipeline.py for compression.
  115. """
  116. # Create test environment
  117. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  118. "--alignment_mode STAR",
  119. "--variant_call_mode GATK",
  120. "--threads 8",
  121. "--plot",
  122. "--reference", self.str_reference_genome,
  123. "--left", self.str_left_file,
  124. "--right",self.str_right_file,
  125. "--out_dir", "_".join([self.str_testing_area,"vanilla_compression"]),
  126. "--vcf", self.str_reference_vcf,
  127. self.str_update_command,
  128. "--compress","archive"])
  129. # Run command
  130. f_success = Commandline.Commandline().func_CMD(str_command)
  131. # Test error
  132. self.assertTrue(f_success, str_command)
  133. def test_rnaseq_mutation_pipeline_for_clean(self):
  134. """
  135. Tests rnaseq_mutation_pipeline.py for clean.
  136. """
  137. # Create test environment
  138. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  139. "--alignment_mode STAR",
  140. "--variant_call_mode GATK",
  141. "--threads 8",
  142. "--plot",
  143. "--reference", self.str_reference_genome,
  144. "--left", self.str_left_file,
  145. "--right", self.str_right_file,
  146. "--out_dir", "_".join([self.str_testing_area,"vanilla_clean"]),
  147. "--vcf", self.str_reference_vcf,
  148. self.str_update_command,
  149. "--clean"])
  150. # Run command
  151. f_success = Commandline.Commandline().func_CMD(str_command)
  152. # Test error
  153. self.assertTrue(f_success, str_command)
  154. def test_rnaseq_mutation_pipeline_for_archive(self):
  155. """
  156. Tests rnaseq_mutation_pipeline.py for archive.
  157. """
  158. # Create test environment
  159. str_copy_dir = os.path.join(self.str_testing_area, "copy_test_runs")
  160. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  161. "--alignment_mode STAR",
  162. "--variant_call_mode GATK",
  163. "--threads 8",
  164. "--plot",
  165. "--reference", self.str_reference_genome,
  166. "--left", self.str_left_file,
  167. "--right", self.str_right_file,
  168. "--out_dir", "_".join([self.str_testing_area,"vanilla_archive"]),
  169. "--vcf",self.str_reference_vcf, self.str_update_command,
  170. "--copy", str_copy_dir])
  171. # Run command
  172. if not os.path.exists(str_copy_dir):
  173. os.mkdir(str_copy_dir)
  174. f_success = Commandline.Commandline().func_CMD(str_command)
  175. # Test error
  176. self.assertTrue(f_success, str_command)
  177. def test_rnaseq_mutation_pipeline_for_realign(self):
  178. """
  179. Tests rnaseq_mutation_pipeline.py for realignment.
  180. """
  181. # Create test environment
  182. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  183. "--alignment_mode STAR",
  184. "--variant_call_mode GATK",
  185. "--threads 8",
  186. "--plot",
  187. "--reference", self.str_reference_genome,
  188. "--left", self.str_left_file,
  189. "--right", self.str_right_file,
  190. "--out_dir", "_".join([self.str_testing_area,"vanilla_realign"]),
  191. "--vcf", self.str_reference_vcf,
  192. self.str_update_command,
  193. "--realign"])
  194. # Run command
  195. f_success = Commandline.Commandline().func_CMD(str_command)
  196. # Test error
  197. self.assertTrue(f_success, str_command)
  198. def test_rnaseq_mutation_pipeline_for_starting_with_bam(self):
  199. """
  200. Tests rnaseq_mutation_pipeline.py for starting with a bam.
  201. """
  202. # Create test environment
  203. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  204. "--alignment_mode STAR",
  205. "--variant_call_mode GATK",
  206. "--threads 8",
  207. "--plot",
  208. "--reference", self.str_reference_genome,
  209. "--left", self.str_left_file,
  210. "--right",self.str_right_file,
  211. "--out_dir", "_".join([self.str_testing_area,"vanilla_bam"]),
  212. "--vcf", self.str_reference_vcf,
  213. self.str_update_command,
  214. "--bam", self.str_input_test_bam])
  215. # Run command
  216. f_success = Commandline.Commandline().func_CMD(str_command)
  217. # Test error
  218. self.assertTrue(f_success, str_command)
  219. def test_rnaseq_mutation_pipeline_for_star_limited(self):
  220. """
  221. Tests rnaseq_mutation_pipeline.py for starting with start limited mode
  222. """
  223. # Create test environment
  224. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  225. "--alignment_mode LIMITED",
  226. "--variant_call_mode GATK",
  227. "--threads 8",
  228. "--plot",
  229. "--reference", self.str_reference_genome,
  230. "--left", self.str_left_file,
  231. "--right", self.str_right_file,
  232. "--out_dir", "_".join([self.str_testing_area,"vanilla_limited"]),
  233. "--vcf", self.str_reference_vcf,
  234. self.str_update_command])
  235. # Run command
  236. f_success = Commandline.Commandline().func_CMD(str_command)
  237. # Test error
  238. self.assertTrue(f_success, str_command)
  239. def test_rnaseq_mutation_pipeline_for_named_log_file(self):
  240. """
  241. Tests rnaseq_mutation_pipeline.py for starting with a named log file.
  242. """
  243. # Create test environment
  244. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  245. "--alignment_mode STAR",
  246. "--variant_call_mode GATK",
  247. "--threads 8",
  248. "--plot",
  249. "--reference", self.str_reference_genome,
  250. "--left", self.str_left_file,
  251. "--right", self.str_right_file,
  252. "--out_dir", "_".join([self.str_testing_area,"vanilla_samtools"]),
  253. "--vcf", self.str_reference_vcf,
  254. self.str_update_command,
  255. "--log", os.path.join("_".join([self.str_testing_area,"vanilla_log"]),"run.log")])
  256. # Run command
  257. f_success = Commandline.Commandline().func_CMD(str_command)
  258. # Test error
  259. self.assertTrue(f_success, str_command)
  260. def test_rnaseq_mutation_pipeline_for_starting_with_premade_index(self):
  261. """
  262. Tests rnaseq_mutation_pipeline.py for starting with a premade index
  263. """
  264. # Create test environment
  265. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  266. "--alignment_mode STAR",
  267. "--variant_call_mode GATK",
  268. "--threads 8",
  269. "--plot",
  270. "--reference", self.str_reference_genome,
  271. "--left", self.str_left_file,
  272. "--right", self.str_right_file,
  273. "--out_dir", "_".join([self.str_testing_area,"vanilla_premade_index"]),
  274. "--vcf", self.str_reference_vcf,
  275. self.str_update_command,
  276. "--index", self.str_input_index])
  277. # Run command
  278. f_success = Commandline.Commandline().func_CMD(str_command)
  279. # Test error
  280. self.assertTrue(f_success, str_command)
  281. def test_rnaseq_mutation_pipeline_for_no_recalibration(self):
  282. """
  283. Tests rnaseq_mutation_pipeline.py for no recalibration
  284. """
  285. # Create test environment
  286. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  287. "--alignment_mode STAR",
  288. "--variant_call_mode GATK",
  289. "--threads 8",
  290. "--plot",
  291. "--reference", self.str_reference_genome,
  292. "--left", self.str_left_file,
  293. "--right", self.str_right_file,
  294. "--out_dir", "_".join([self.str_testing_area,"vanilla_no_recal"]),
  295. "--vcf", self.str_reference_vcf,
  296. self.str_update_command,
  297. "--recalibrate_sam"])
  298. # Run command
  299. f_success = Commandline.Commandline().func_CMD(str_command)
  300. # Test error
  301. self.assertTrue(f_success, str_command)
  302. def test_rnaseq_mutation_pipeline_for_move(self):
  303. """
  304. Tests rnaseq_mutation_pipeline.py for moving files
  305. """
  306. # Create test environment
  307. str_move_dir = os.path.join(self.str_testing_area, "move_test_runs")
  308. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  309. "--alignment_mode STAR",
  310. "--variant_call_mode GATK",
  311. "--threads 8",
  312. "--plot",
  313. "--reference", self.str_reference_genome,
  314. "--left", self.str_left_file,
  315. "--right", self.str_right_file,
  316. "--out_dir", "_".join([self.str_testing_area,"vanilla_no_move"]),
  317. "--vcf", self.str_reference_vcf,
  318. self.str_update_command,
  319. "--move", str_move_dir])
  320. # Run command
  321. if not os.path.exists(str_move_dir):
  322. os.mkdir(str_move_dir)
  323. f_success = Commandline.Commandline().func_CMD(str_command)
  324. # Test error
  325. self.assertTrue(f_success, str_command)
  326. def test_rnaseq_mutation_pipeline_for_no_filtering(self):
  327. """
  328. Tests rnaseq_mutation_pipeline.py for a run with no filtering.
  329. """
  330. # Create test environment
  331. str_command = " ".join(["python rnaseq_mutation_pipeline.py",
  332. "--alignment_mode STAR",
  333. "--variant_call_mode GATK",
  334. "--threads 8",
  335. "--plot",
  336. "--reference", self.str_reference_genome,
  337. "--left", self.str_left_file,
  338. "--right", self.str_right_file,
  339. "--variant_filtering_mode NONE",
  340. "--out_dir", "_".join([self.str_testing_area,"vanilla_samtools"]),
  341. "--vcf", self.str_reference_vcf,
  342. self.str_update_command])
  343. # Run command
  344. f_success = Commandline.Commandline().func_CMD(str_command)
  345. # Test error
  346. self.assertTrue(f_success, str_command)
  347. # Creates a suite of tests
  348. def suite():
  349. return unittest.TestLoader().loadTestsFromTestCase(FunctionalTester)

FunctionalTester.py at commit 42855af, under BSD-3-Clause · at the source

Overview

  1. Faculty of Medicine, Institute of Pathology, University of Ljubljana,Ljubljana, Slovenia
Institutions: University of Ljubljana (Slovenia)
Journal: Cancer immunology, immunotherapy : CII, volume 75, issue 5, article 149
Dates: received 16 January 2026; accepted 6 April 2026; published online 21 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1007/s00262-026-04390-3 · PMID 42012534 · PMCID PMC13100171 · OpenAlex W7155094685
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), other condition (population), cellular / molecular (subfield)
Methods: Statistics, Connectivity
Keywords: Glioblastoma, Tumor antigens, Computational immunology, HLA class I, Transcriptome sequencing
MeSH: Antigens, Neoplasm*, Brain Neoplasms*, Glioblastoma*, Transcriptome*, Biomarkers, Tumor, Gene Expression Profiling, Humans, Mutation (* major topic)
Topic: Glioma Diagnosis and Treatment (Genetics, Medicine), according to OpenAlex
Citations: not cited yet (Europe PMC); 49 references in the paper

Abstract

Glioblastoma (GBM) is an aggressive brain tumour with limited responsiveness to current immunotherapeutic approaches, partly due to its low mutational burden and intra-tumour heterogeneity. A systematic understanding of the tumour antigen landscape is therefore essential for advancing tumour immunology and supporting rational development of immunotherapeutic strategies. In this study, we performed whole-transcriptome sequencing of RNA extracted from 79 formalin-fixed paraffin-embedded (FFPE) IDH-wildtype GBM samples to systematically identify and prioritise candidate tumour antigens derived from three sources: single-nucleotide variants (SNVs), overexpressed tumour-associated antigens (TAAs), and gene fusion events. Candidate peptides were evaluated using integrated computational criteria, including transcript expression, predicted antigen processing features, peptide–HLA binding affinity and stability. Across the cohort, mutation-derived tumor-specific antigens (TSAs) were largely private to individual samples, whereas TAAs constituted a larger and more recurrent candidate pool. Despite comparable predicted binding characteristics across antigen classes, recurrence patterns differed substantially, reflecting their distinct biological origins. Fusion-derived candidates were rare and sample-specific. Predicted peptide presentation was disproportionately associated with a limited subset of HLA class I alleles. Collectively, this study provides a systematically prioritized catalogue of transcriptionally expressed GBM antigen candidates and offers a comparative evaluation of mutation-, expression-, and fusion-derived antigen sources within a unified transcriptome-based framework.

Supplementary Information: The online version contains supplementary material available at 10.1007/s00262-026-04390-3.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

NCIP/ctat-mutations

License: BSD-3-Clause
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 42855afcc771db09819388ef71fb91f3a83a8415, 13 January 2026
Languages: Python (46), Shell (6), R (5), Perl (5)
Size: 172 files, 62 scripts
Software Heritage: not archived
Found in: the text, “HLA typing, mutation detection”
Holds: README, license file, environment (Docker/Dockerfile), tests
Not found: CITATION.cff, continuous integration, documentation
Tools: Matplotlib (6 files), pandas (6 files), NumPy (5 files), SAMtools (4 files), scikit-learn (3 files), BEDTools (2 files), pysam (2 files), SciPy (2 files), statsmodels (2 files), XGBoost (2 files), BCFtools (1 file), ggplot2 (1 file), reshape2 (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
64 files

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 62 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

The data presented in this study are available on request from the corresponding author. The normal tissue dataset analysed in this study was obtained from: [https://www.gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression#bulk_tissue_expression-gtex_analysis_v10-rna-seq](https:/www.gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression), the Genotype-Tissue Expression (GTEx) Portal on 08/25/2025. The GTEx Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS.

Reproduced under the paper's license (CC BY), from the paper cited above.

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 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 5 keywords, 8 MeSH terms, 1 funder, 48 references.

Cite

This paper

Kert, Š., Pižem, J., Petrin, S., Bošnjak, M., Jerala, M., Matjašič, A., & Zupan, A. (2026). Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes. Cancer immunology, immunotherapy : CII, 75(5), 149. https://doi.org/10.1007/s00262-026-04390-3

BibTeX

@article{kert2026identification,
author = {Kert, Špela and Pižem, Jože and Petrin, Sara and Bošnjak, Matic and Jerala, Miha and Matjašič, Alenka and Zupan, Andrej},
title = {{Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes}},
journal = {Cancer immunology, immunotherapy : CII},
year = {2026},
month = apr,
volume = {75},
number = {5},
pages = {149},
publisher = {Springer},
issn = {0340-7004},
doi = {10.1007/s00262-026-04390-3},
url = {https://doi.org/10.1007/s00262-026-04390-3},
pmid = {42012534},
pmcid = {PMC13100171}
}

RIS

TY - JOUR
AU - Kert, Špela
AU - Pižem, Jože
AU - Petrin, Sara
AU - Bošnjak, Matic
AU - Jerala, Miha
AU - Matjašič, Alenka
AU - Zupan, Andrej
TI - Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes
T2 - Cancer immunology, immunotherapy : CII
J2 - Cancer Immunol Immunother
PY - 2026
DA - 2026/04/21
VL - 75
IS - 5
SP - 149
SN - 0340-7004
PB - Springer
DO - 10.1007/s00262-026-04390-3
UR - https://doi.org/10.1007/s00262-026-04390-3
LA - en
ER -

CSL-JSON

{
"id": "10.1007/s00262-026-04390-3",
"type": "article-journal",
"title": "Identification and prioritisation of tumour antigen candidates from 79 glioblastoma transcriptomes",
"container-title": "Cancer immunology, immunotherapy : CII",
"author": [
{
"family": "Kert",
"given": "Špela"
},
{
"family": "Pižem",
"given": "Jože"
},
{
"family": "Petrin",
"given": "Sara"
},
{
"family": "Bošnjak",
"given": "Matic"
},
{
"family": "Jerala",
"given": "Miha"
},
{
"family": "Matjašič",
"given": "Alenka"
},
{
"family": "Zupan",
"given": "Andrej"
}
],
"container-title-short": "Cancer Immunol Immunother",
"volume": "75",
"issue": "5",
"page": "149",
"DOI": "10.1007/s00262-026-04390-3",
"PMID": "42012534",
"PMCID": "PMC13100171",
"ISSN": "0340-7004",
"publisher": "Springer",
"URL": "https://doi.org/10.1007/s00262-026-04390-3",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
21
]
]
}
}

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