Mutations#

The module mutations provides functions related to Mutations section of cBioPortal Web Public API.

pybioportal.mutations.fetch_muts_in_mol_prof(molecular_profile_id, entrez_gene_ids=None, sample_ids=None, sample_list_id=None, projection='SUMMARY', direction='ASC', pageNumber=0, pageSize=10000000, sortBy=None)#

Fetch mutations in a molecular profile.

Parameters:

  • molecular_profile_id (str) – Molecular Profile ID (e.g., “brca_tcga_mutations”).

  • entrez_gene_ids (List of str) – List ID and Entrez Gene IDs (e.g., [“TCGA-AR-A1AR-01”,”TCGA-BH-A1EO-01”]).

  • sample_ids (List of str) – List of Sample IDs (e.g., [“1005”, “1020”]).

  • sample_list_id (str) – Sample List ID (e.g., “brca_tcga_all”).

  • projection (str) –

    Level of detail of the response.

    Possible values:

    • ”DETAILED”: Detailed information.

    • ”ID”: Information with only IDs.

    • ”META”: Metadata information.

    • ”SUMMARY”: Summary information (default).

  • direction (str) –

    Direction of the sort.

    Possible values:

    • ”ASC”: Ascending (default).

    • ”DESC”: Descending.

  • pageNumber (int) –

    Page number of the result list.

    • Minimum value is 0.

  • pageSize (int) –

    Page size of the result list.

    • Minimum value is 1, maximum value is 10000000.

  • sortBy (str) –

    Name of the property that the result list is sorted by.

    Possible values:

    • ”aminoAcidChange”

    • ”center”

    • ”endPosition”

    • ”entrezGeneId”

    • ”keyword”

    • ”mutationStatus”

    • ”mutationType”

    • ”ncbiBuild”

    • ”normalAltCount”

    • ”normalRefCount”

    • ”proteinChange”

    • ”proteinPosEnd”

    • ”proteinPosStart”

    • ”referenceAllele”

    • ”refseqMrnaId”

    • ”startPosition”

    • ”tumorAltCount”

    • ”tumorRefCount”

    • ”validationStatus”

    • ”variantAllele”

    • ”variantType”

Returns:

A DataFrame containing mutations in the molecular profile.

Return type:

pandas.DataFrame

pybioportal.mutations.fetch_muts_in_multiple_mol_profs(entrez_gene_ids=None, molecular_profile_ids=None, sample_molecular_identifiers=None, projection='SUMMARY', direction='ASC', pageNumber=0, pageSize=10000000, sortBy=None)#

Fetch mutations in multiple molecular profiles by sample IDs.

Parameters:

  • entrez_gene_ids (list of str) – List of Entrez Gene IDs (e.g. [“672”,”675”]).

  • molecular_profile_ids (list of str) – List of Molecular Profile IDs (e.g. [“brca_tcga_mutations”, “acc_tcga_mutations”]).

  • sample_molecular_identifiers – List of Molecular Profile ID / Sample ID pairs.

  • projection (str) –

    Level of detail of the response.

    Possible values:

    • ”DETAILED”: Detailed information.

    • ”ID”: Information with only IDs.

    • ”META”: Metadata information.

    • ”SUMMARY”: Summary information (default).

  • direction (str) –

    Direction of the sort.

    Possible values:

    • ”ASC”: Ascending (default).

    • ”DESC”: Descending.

  • pageNumber (int) –

    Page number of the result list.

    • Minimum value is 0.

  • pageSize (int) –

    Page size of the result list.

    • Minimum value is 1, maximum value is 10000000.

  • sortBy (str) –

    Name of the property that the result list is sorted by.

    Possible values:

    • ”aminoAcidChange”

    • ”center”

    • ”endPosition”

    • ”entrezGeneId”

    • ”keyword”

    • ”mutationStatus”

    • ”mutationType”

    • ”ncbiBuild”

    • ”normalAltCount”

    • ”normalRefCount”

    • ”proteinChange”

    • ”proteinPosEnd”

    • ”proteinPosStart”

    • ”referenceAllele”

    • ”refseqMrnaId”

    • ”startPosition”

    • ”tumorAltCount”

    • ”tumorRefCount”

    • ”validationStatus”

    • ”variantAllele”

    • ”variantType”

Returns:

A DataFrame containing mutations in the specified molecular profiles.

Return type:

pandas.DataFrame

pybioportal.mutations.get_muts_in_mol_prof_by_sample_list_id(molecular_profile_id, sample_list_id, entrez_gene_id=None, projection='SUMMARY', direction='ASC', pageNumber=0, pageSize=10000000, sortBy=None)#

Get mutations in a molecular profile by Sample List ID.

Parameters:

  • molecular_profile_id (str) – Molecular Profile ID (e.g., “acc_tcga_mutations”).

  • sample_list_id (str) – Sample List ID (e.g., “acc_tcga_all”).

  • projection (str) –

    Level of detail of the response.

    Possible values:

    • ”DETAILED”: Detailed information.

    • ”ID”: Information with only IDs.

    • ”META”: Metadata information.

    • ”SUMMARY”: Summary information (default).

  • entrez_gene_id (str) – Entrez Gene ID (e.g., “1”).

  • direction (str) –

    Direction of the sort.

    Possible values:

    • ”ASC”: Ascending (default).

    • ”DESC”: Descending.

  • pageNumber (int) –

    Page number of the result list.

    • Minimum value is 0.

  • pageSize (int) –

    Page size of the result list.

    • Minimum value is 1, maximum value is 10000000.

  • sortBy (str) –

    Name of the property that the result list is sorted by.

    Possible values:

    • ”aminoAcidChange”

    • ”center”

    • ”endPosition”

    • ”entrezGeneId”

    • ”keyword”

    • ”mutationStatus”

    • ”mutationType”

    • ”ncbiBuild”

    • ”normalAltCount”

    • ”normalRefCount”

    • ”proteinChange”

    • ”proteinPosEnd”

    • ”proteinPosStart”

    • ”referenceAllele”

    • ”refseqMrnaId”

    • ”startPosition”

    • ”tumorAltCount”

    • ”tumorRefCount”

    • ”validationStatus”

    • ”variantAllele”

    • ”variantType”

Returns:

A DataFrame containing mutations in the molecular profile.

Return type:

pandas.DataFrame

Examples#

from pybioportal import mutations as mts

df1 = mts.get_muts_in_mol_prof_by_sample_list_id(molecular_profile_id="brca_tcga_mutations",
                                                 sample_list_id="brca_tcga_all",
                                                 entrez_gene_id="672")
df1
uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId entrezGeneId studyId center mutationStatus validationStatus ... proteinChange mutationType ncbiBuild variantType keyword chr variantAllele refseqMrnaId proteinPosStart proteinPosEnd
0 VENHQS1BMi1BNFMwLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BNFMwOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A4S0-01 TCGA-A2-A4S0 672 brca_tcga genome.wustl.edu Somatic Untested ... K50T Missense_Mutation GRCh37 SNP BRCA1 K50 missense 17 G NM_007294.3 50 50
1 VENHQS1FMi1BMUw5LTAxOmJyY2FfdGNnYQ VENHQS1FMi1BMUw5OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-E2-A1L9-01 TCGA-E2-A1L9 672 brca_tcga genome.wustl.edu Somatic Untested ... S1027I Missense_Mutation GRCh37 SNP BRCA1 S1027 missense 17 A NM_007294.3 1027 1027
2 VENHQS1CSC1BMFdBLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMFdBOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A0WA-01 TCGA-BH-A0WA 672 brca_tcga genome.wustl.edu Somatic Untested ... X1559_splice Splice_Site GRCh37 SNP BRCA1 truncating 17 T NM_007294.3 1559 1559
3 VENHQS1FOS1BMU5DLTAxOmJyY2FfdGNnYQ VENHQS1FOS1BMU5DOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-E9-A1NC-01 TCGA-E9-A1NC 672 brca_tcga genome.wustl.edu Somatic Untested ... Q139* Nonsense_Mutation GRCh37 SNP BRCA1 truncating 17 A NM_007294.3 139 139
4 VENHQS1DOC1BMTJULTAxOmJyY2FfdGNnYQ VENHQS1DOC1BMTJUOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-C8-A12T-01 TCGA-C8-A12T 672 brca_tcga genome.wustl.edu Somatic Untested ... D1344H Missense_Mutation GRCh37 SNP BRCA1 D1344 missense 17 G NM_007294.3 1344 1344
5 VENHQS1MTC1BNVlQLTAxOmJyY2FfdGNnYQ VENHQS1MTC1BNVlQOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-LL-A5YP-01 TCGA-LL-A5YP 672 brca_tcga genome.wustl.edu Somatic Untested ... D96H Missense_Mutation GRCh37 SNP BRCA1 D96 missense 17 G NM_007294.3 96 96
6 VENHQS1BTy1BMUtSLTAxOmJyY2FfdGNnYQ VENHQS1BTy1BMUtSOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AO-A1KR-01 TCGA-AO-A1KR 672 brca_tcga genome.wustl.edu Somatic Untested ... C644del In_Frame_Del GRCh37 DEL BRCA1 644-644 deletion 17 - NM_007294.3 644 644
7 VENHQS1BMS1BMFNJLTAxOmJyY2FfdGNnYQ VENHQS1BMS1BMFNJOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A1-A0SI-01 TCGA-A1-A0SI 672 brca_tcga genome.wustl.edu Somatic Untested ... E9Q Missense_Mutation GRCh37 SNP BRCA1 E9 missense 17 G NM_007294.3 9 9
8 VENHQS1BTi1BMFhVLTAxOmJyY2FfdGNnYQ VENHQS1BTi1BMFhVOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AN-A0XU-01 TCGA-AN-A0XU 672 brca_tcga genome.wustl.edu Somatic Untested ... G1788V Missense_Mutation GRCh37 SNP BRCA1 G1788 missense 17 A NM_007294.3 1788 1788
9 VENHQS1BMi1BMjVCLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BMjVCOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A25B-01 TCGA-A2-A25B 672 brca_tcga genome.wustl.edu Somatic Untested ... E720* Nonsense_Mutation GRCh37 SNP BRCA1 truncating 17 A NM_007294.3 720 720
10 VENHQS1FVy1BMkZSLTAxOmJyY2FfdGNnYQ VENHQS1FVy1BMkZSOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-EW-A2FR-01 TCGA-EW-A2FR 672 brca_tcga genome.wustl.edu Somatic Untested ... D366N Missense_Mutation GRCh37 SNP BRCA1 D366 missense 17 T NM_007294.3 366 366
11 VENHQS1EOC1BMjdNLTAxOmJyY2FfdGNnYQ VENHQS1EOC1BMjdNOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-D8-A27M-01 TCGA-D8-A27M 672 brca_tcga genome.wustl.edu Somatic Untested ... P1614Qfs*19 Frame_Shift_Del GRCh37 DEL BRCA1 truncating 17 - NM_007294.3 1614 1614
12 VENHQS1QRS1BNURFLTAxOmJyY2FfdGNnYQ VENHQS1QRS1BNURFOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-PE-A5DE-01 TCGA-PE-A5DE 672 brca_tcga genome.wustl.edu Somatic Untested ... E1419K Missense_Mutation GRCh37 SNP BRCA1 E1419 missense 17 T NM_007294.3 1419 1419

13 rows × 25 columns

df2a = mts.fetch_muts_in_mol_prof(molecular_profile_id="brca_tcga_mutations",
                                  entrez_gene_ids=["1005", "1020"],
                                  sample_ids = ["TCGA-AR-A1AR-01","TCGA-BH-A1EO-01"])
df2a
uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId entrezGeneId studyId center mutationStatus validationStatus ... proteinChange mutationType ncbiBuild variantType keyword chr variantAllele refseqMrnaId proteinPosStart proteinPosEnd
0 VENHQS1CSC1BMUVPLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMUVPOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A1EO-01 TCGA-BH-A1EO 1005 brca_tcga genome.wustl.edu Somatic Untested ... R695Q Missense_Mutation GRCh37 SNP CDH7 R695 missense 18 A NM_004361.2 695 695
1 VENHQS1CSC1BMUVPLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMUVPOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A1EO-01 TCGA-BH-A1EO 1020 brca_tcga genome.wustl.edu Somatic Untested ... V162L Missense_Mutation GRCh37 SNP CDK5 V162 missense 7 A NM_004935.3 162 162

2 rows × 25 columns

df2b = mts.fetch_muts_in_mol_prof(molecular_profile_id="brca_tcga_mutations",
                                  entrez_gene_ids=["1005", "1020"],
                                  sample_list_id="brca_tcga_all")
df2b
uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId entrezGeneId studyId center mutationStatus validationStatus ... proteinChange mutationType ncbiBuild variantType keyword chr variantAllele refseqMrnaId proteinPosStart proteinPosEnd
0 VENHQS1CSC1BMUVPLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMUVPOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A1EO-01 TCGA-BH-A1EO 1005 brca_tcga genome.wustl.edu Somatic Untested ... R695Q Missense_Mutation GRCh37 SNP CDH7 R695 missense 18 A NM_004361.2 695 695
1 VENHQS1PTC1BNUQ4LTAxOmJyY2FfdGNnYQ VENHQS1PTC1BNUQ4OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-OL-A5D8-01 TCGA-OL-A5D8 1005 brca_tcga genome.wustl.edu Somatic Untested ... S556* Nonsense_Mutation GRCh37 SNP CDH7 truncating 18 A NM_004361.2 556 556
2 VENHQS1EOC1BMUpMLTAxOmJyY2FfdGNnYQ VENHQS1EOC1BMUpMOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-D8-A1JL-01 TCGA-D8-A1JL 1005 brca_tcga genome.wustl.edu Somatic Untested ... G78A Missense_Mutation GRCh37 SNP CDH7 G78 missense 18 C NM_004361.2 78 78
3 VENHQS1BTi1BMDQ2LTAxOmJyY2FfdGNnYQ VENHQS1BTi1BMDQ2OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AN-A046-01 TCGA-AN-A046 1005 brca_tcga genome.wustl.edu Somatic Untested ... T178M Missense_Mutation GRCh37 SNP CDH7 T178 missense 18 T NM_004361.2 178 178
4 VENHQS1BTi1BMDQ2LTAxOmJyY2FfdGNnYQ VENHQS1BTi1BMDQ2OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AN-A046-01 TCGA-AN-A046 1005 brca_tcga genome.wustl.edu Somatic Untested ... R264Q Missense_Mutation GRCh37 SNP CDH7 R264 missense 18 A NM_004361.2 264 264
5 VENHQS1CSC1BMUVPLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMUVPOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A1EO-01 TCGA-BH-A1EO 1020 brca_tcga genome.wustl.edu Somatic Untested ... V162L Missense_Mutation GRCh37 SNP CDK5 V162 missense 7 A NM_004935.3 162 162
6 VENHQS1EOC1BMUpBLTAxOmJyY2FfdGNnYQ VENHQS1EOC1BMUpBOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-D8-A1JA-01 TCGA-D8-A1JA 1020 brca_tcga genome.wustl.edu Somatic Untested ... E101Q Missense_Mutation GRCh37 SNP CDK5 E101 missense 7 G NM_004935.3 101 101

7 rows × 25 columns

df3a = mts.fetch_muts_in_multiple_mol_profs(entrez_gene_ids=["672","675"],
                                            molecular_profile_ids=["brca_tcga_mutations", "acc_tcga_mutations"])
df3a
uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId entrezGeneId studyId center mutationStatus validationStatus ... proteinChange mutationType ncbiBuild variantType chr variantAllele refseqMrnaId proteinPosStart proteinPosEnd keyword
0 VENHQS1PUi1BNUxFLTAxOmFjY190Y2dh VENHQS1PUi1BNUxFOmFjY190Y2dh acc_tcga_mutations TCGA-OR-A5LE-01 TCGA-OR-A5LE 675 acc_tcga bcgsc.ca Somatic Untested ... V733_L734insFFF In_Frame_Ins GRCh37 INS 13 TCTTCTTCT NA 733 734 NaN
1 VENHQS1BMi1BNFMwLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BNFMwOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A4S0-01 TCGA-A2-A4S0 672 brca_tcga genome.wustl.edu Somatic Untested ... K50T Missense_Mutation GRCh37 SNP 17 G NM_007294.3 50 50 BRCA1 K50 missense
2 VENHQS1FMi1BMUw5LTAxOmJyY2FfdGNnYQ VENHQS1FMi1BMUw5OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-E2-A1L9-01 TCGA-E2-A1L9 672 brca_tcga genome.wustl.edu Somatic Untested ... S1027I Missense_Mutation GRCh37 SNP 17 A NM_007294.3 1027 1027 BRCA1 S1027 missense
3 VENHQS1CSC1BMFdBLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMFdBOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A0WA-01 TCGA-BH-A0WA 672 brca_tcga genome.wustl.edu Somatic Untested ... X1559_splice Splice_Site GRCh37 SNP 17 T NM_007294.3 1559 1559 BRCA1 truncating
4 VENHQS1FOS1BMU5DLTAxOmJyY2FfdGNnYQ VENHQS1FOS1BMU5DOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-E9-A1NC-01 TCGA-E9-A1NC 672 brca_tcga genome.wustl.edu Somatic Untested ... Q139* Nonsense_Mutation GRCh37 SNP 17 A NM_007294.3 139 139 BRCA1 truncating
5 VENHQS1DOC1BMTJULTAxOmJyY2FfdGNnYQ VENHQS1DOC1BMTJUOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-C8-A12T-01 TCGA-C8-A12T 672 brca_tcga genome.wustl.edu Somatic Untested ... D1344H Missense_Mutation GRCh37 SNP 17 G NM_007294.3 1344 1344 BRCA1 D1344 missense
6 VENHQS1MTC1BNVlQLTAxOmJyY2FfdGNnYQ VENHQS1MTC1BNVlQOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-LL-A5YP-01 TCGA-LL-A5YP 672 brca_tcga genome.wustl.edu Somatic Untested ... D96H Missense_Mutation GRCh37 SNP 17 G NM_007294.3 96 96 BRCA1 D96 missense
7 VENHQS1BTy1BMUtSLTAxOmJyY2FfdGNnYQ VENHQS1BTy1BMUtSOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AO-A1KR-01 TCGA-AO-A1KR 672 brca_tcga genome.wustl.edu Somatic Untested ... C644del In_Frame_Del GRCh37 DEL 17 - NM_007294.3 644 644 BRCA1 644-644 deletion
8 VENHQS1BMS1BMFNJLTAxOmJyY2FfdGNnYQ VENHQS1BMS1BMFNJOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A1-A0SI-01 TCGA-A1-A0SI 672 brca_tcga genome.wustl.edu Somatic Untested ... E9Q Missense_Mutation GRCh37 SNP 17 G NM_007294.3 9 9 BRCA1 E9 missense
9 VENHQS1BTi1BMFhVLTAxOmJyY2FfdGNnYQ VENHQS1BTi1BMFhVOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AN-A0XU-01 TCGA-AN-A0XU 672 brca_tcga genome.wustl.edu Somatic Untested ... G1788V Missense_Mutation GRCh37 SNP 17 A NM_007294.3 1788 1788 BRCA1 G1788 missense
10 VENHQS1BMi1BMjVCLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BMjVCOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A25B-01 TCGA-A2-A25B 672 brca_tcga genome.wustl.edu Somatic Untested ... E720* Nonsense_Mutation GRCh37 SNP 17 A NM_007294.3 720 720 BRCA1 truncating
11 VENHQS1FVy1BMkZSLTAxOmJyY2FfdGNnYQ VENHQS1FVy1BMkZSOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-EW-A2FR-01 TCGA-EW-A2FR 672 brca_tcga genome.wustl.edu Somatic Untested ... D366N Missense_Mutation GRCh37 SNP 17 T NM_007294.3 366 366 BRCA1 D366 missense
12 VENHQS1EOC1BMjdNLTAxOmJyY2FfdGNnYQ VENHQS1EOC1BMjdNOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-D8-A27M-01 TCGA-D8-A27M 672 brca_tcga genome.wustl.edu Somatic Untested ... P1614Qfs*19 Frame_Shift_Del GRCh37 DEL 17 - NM_007294.3 1614 1614 BRCA1 truncating
13 VENHQS1QRS1BNURFLTAxOmJyY2FfdGNnYQ VENHQS1QRS1BNURFOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-PE-A5DE-01 TCGA-PE-A5DE 672 brca_tcga genome.wustl.edu Somatic Untested ... E1419K Missense_Mutation GRCh37 SNP 17 T NM_007294.3 1419 1419 BRCA1 E1419 missense
14 VENHQS1BOC1BMDdJLTAxOmJyY2FfdGNnYQ VENHQS1BOC1BMDdJOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A8-A07I-01 TCGA-A8-A07I 675 brca_tcga genome.wustl.edu Somatic Untested ... D1355Y Missense_Mutation GRCh37 SNP 13 T NA 1355 1355 BRCA2 D1355 missense
15 VENHQS1EOC1BMUpQLTAxOmJyY2FfdGNnYQ VENHQS1EOC1BMUpQOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-D8-A1JP-01 TCGA-D8-A1JP 675 brca_tcga genome.wustl.edu Somatic Untested ... L1965Ffs*39 Frame_Shift_Del GRCh37 DEL 13 - NA 1965 1965 BRCA2 truncating
16 VENHQS1BOC1BMDhMLTAxOmJyY2FfdGNnYQ VENHQS1BOC1BMDhMOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A8-A08L-01 TCGA-A8-A08L 675 brca_tcga genome.wustl.edu Somatic Untested ... X2602_splice Splice_Site GRCh37 SNP 13 A NA 2602 2602 BRCA2 truncating
17 VENHQS1EOC1BMjdHLTAxOmJyY2FfdGNnYQ VENHQS1EOC1BMjdHOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-D8-A27G-01 TCGA-D8-A27G 675 brca_tcga genome.wustl.edu Somatic Untested ... E2175Q Missense_Mutation GRCh37 SNP 13 C NA 2175 2175 BRCA2 E2175 missense
18 VENHQS1BTi1BMEFULTAxOmJyY2FfdGNnYQ VENHQS1BTi1BMEFUOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AN-A0AT-01 TCGA-AN-A0AT 675 brca_tcga genome.wustl.edu Somatic Untested ... E2650Q Missense_Mutation GRCh37 SNP 13 C NA 2650 2650 BRCA2 E2650 missense
19 VENHQS1BMi1BMFQwLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BMFQwOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A0T0-01 TCGA-A2-A0T0 675 brca_tcga genome.wustl.edu Somatic Untested ... L2926* Nonsense_Mutation GRCh37 SNP 13 G NA 2926 2926 BRCA2 truncating
20 VENHQS1DOC1BMTJULTAxOmJyY2FfdGNnYQ VENHQS1DOC1BMTJUOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-C8-A12T-01 TCGA-C8-A12T 675 brca_tcga genome.wustl.edu Somatic Untested ... E3177Q Missense_Mutation GRCh37 SNP 13 C NA 3177 3177 BRCA2 E3177 missense
21 VENHQS1BOC1BMDhCLTAxOmJyY2FfdGNnYQ VENHQS1BOC1BMDhCOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A8-A08B-01 TCGA-A8-A08B 675 brca_tcga genome.wustl.edu Somatic Untested ... V1270del In_Frame_Del GRCh37 DEL 13 - NA 1268 1270 BRCA2 1270-1270 deletion
22 VENHQS1BUi1BMUFJLTAxOmJyY2FfdGNnYQ VENHQS1BUi1BMUFJOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AR-A1AI-01 TCGA-AR-A1AI 675 brca_tcga genome.wustl.edu Somatic Untested ... R2336C Missense_Mutation GRCh37 SNP 13 T NA 2336 2336 BRCA2 R2336 missense
23 VENHQS1CSC1BMEhGLTAxOmJyY2FfdGNnYQ VENHQS1CSC1BMEhGOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-BH-A0HF-01 TCGA-BH-A0HF 675 brca_tcga genome.wustl.edu Somatic Untested ... S879F Missense_Mutation GRCh37 SNP 13 T NA 879 879 BRCA2 S879 missense
24 VENHQS1BQy1BMjNILTAxOmJyY2FfdGNnYQ VENHQS1BQy1BMjNIOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AC-A23H-01 TCGA-AC-A23H 675 brca_tcga genome.wustl.edu Somatic Untested ... D687H Missense_Mutation GRCh37 SNP 13 C NA 687 687 BRCA2 D687 missense
25 VENHQS1BQy1BMjNILTAxOmJyY2FfdGNnYQ VENHQS1BQy1BMjNIOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AC-A23H-01 TCGA-AC-A23H 675 brca_tcga genome.wustl.edu Somatic Untested ... D1033H Missense_Mutation GRCh37 SNP 13 C NA 1033 1033 BRCA2 D1033 missense
26 VENHQS1FVy1BMVBFLTAxOmJyY2FfdGNnYQ VENHQS1FVy1BMVBFOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-EW-A1PE-01 TCGA-EW-A1PE 675 brca_tcga genome.wustl.edu Somatic Untested ... E1158Q Missense_Mutation GRCh37 SNP 13 C NA 1158 1158 BRCA2 E1158 missense
27 VENHQS1FVy1BMVBFLTAxOmJyY2FfdGNnYQ VENHQS1FVy1BMVBFOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-EW-A1PE-01 TCGA-EW-A1PE 675 brca_tcga genome.wustl.edu Somatic Untested ... K1191N Missense_Mutation GRCh37 SNP 13 C NA 1191 1191 BRCA2 K1191 missense
28 VENHQS1BMi1BMjVGLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BMjVGOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A25F-01 TCGA-A2-A25F 675 brca_tcga genome.wustl.edu Somatic Untested ... Y3049S Missense_Mutation GRCh37 SNP 13 C NA 3049 3049 BRCA2 Y3049 missense
29 VENHQS1BTy1BMTI0LTAxOmJyY2FfdGNnYQ VENHQS1BTy1BMTI0OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AO-A124-01 TCGA-AO-A124 675 brca_tcga genome.wustl.edu Somatic Untested ... C3304S Missense_Mutation GRCh37 SNP 13 C NA 3304 3304 BRCA2 C3304 missense
30 VENHQS1BTi1BMDQ2LTAxOmJyY2FfdGNnYQ VENHQS1BTi1BMDQ2OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-AN-A046-01 TCGA-AN-A046 675 brca_tcga genome.wustl.edu Somatic Untested ... E3342K Missense_Mutation GRCh37 SNP 13 A NA 3342 3342 BRCA2 E3342 missense

31 rows × 27 columns

df3b = mts.fetch_muts_in_multiple_mol_profs(entrez_gene_ids=["672","675"],
                                            sample_molecular_identifiers=[
                                                        {"molecular_profile_id": "brca_tcga_mutations",
                                                         "sample_ids": ["TCGA-A2-A4S0-01","TCGA-E2-A1L9-01"]},
                                                        {"molecular_profile_id": "acc_tcga_mutations",
                                                         "sample_ids": ["TCGA-OR-A5LE-01"]}
                                                        ])
df3b
uniqueSampleKey uniquePatientKey molecularProfileId sampleId patientId entrezGeneId studyId center mutationStatus validationStatus ... proteinChange mutationType ncbiBuild variantType chr variantAllele refseqMrnaId proteinPosStart proteinPosEnd keyword
0 VENHQS1PUi1BNUxFLTAxOmFjY190Y2dh VENHQS1PUi1BNUxFOmFjY190Y2dh acc_tcga_mutations TCGA-OR-A5LE-01 TCGA-OR-A5LE 675 acc_tcga bcgsc.ca Somatic Untested ... V733_L734insFFF In_Frame_Ins GRCh37 INS 13 TCTTCTTCT NA 733 734 NaN
1 VENHQS1FMi1BMUw5LTAxOmJyY2FfdGNnYQ VENHQS1FMi1BMUw5OmJyY2FfdGNnYQ brca_tcga_mutations TCGA-E2-A1L9-01 TCGA-E2-A1L9 672 brca_tcga genome.wustl.edu Somatic Untested ... S1027I Missense_Mutation GRCh37 SNP 17 A NM_007294.3 1027 1027 BRCA1 S1027 missense
2 VENHQS1BMi1BNFMwLTAxOmJyY2FfdGNnYQ VENHQS1BMi1BNFMwOmJyY2FfdGNnYQ brca_tcga_mutations TCGA-A2-A4S0-01 TCGA-A2-A4S0 672 brca_tcga genome.wustl.edu Somatic Untested ... K50T Missense_Mutation GRCh37 SNP 17 G NM_007294.3 50 50 BRCA1 K50 missense

3 rows × 27 columns