Philips ISPM Aberration

The table onc_philips_mtb_aberrations contains genomic testing information from the Philips IntelliSpace Precision Medicine (ISPM) genomics database at Stanford. The fields in this table are related to genomic testing details about each sample, as well as the specimen accession number which can be used to link to the Philips ISPM Orders table.

Table Columns

column name	type	phi	phi-scrubbing operation
aberration_class	STRING
aberration_type	STRING
accession_number	STRING	Yes	Hash
chrom	STRING
hgnc_gene	STRING
id	STRING	Yes	Stable Between Data Refreshes
is_selected_aberration_flag	INT64
person_id	INT64	Yes	Stable Between Data Refreshes
stanford_aa_change	STRING
stanford_break_1	STRING
stanford_break_2	STRING
stanford_gene	STRING
stanford_hgvs_coding	STRING
stanford_hgvs_genomic	STRING
stanford_hgvs_protein	STRING
stanford_interpretation	STRING	Yes	TiDE
stanford_minimum_copies	STRING
stanford_pathogenicity	STRING
stanford_patient_uid	STRING	Yes	Del
stanford_region_1	STRING
stanford_transcript	STRING
stanford_vaf	STRING
stanford_variant	STRING

Columns Description

aberration_class

Aberration class (No description available)

aberration_type

Aberration type (No description available)

accession_number

Identifier for the specimen. This field can be used to link to the pat_diag_orders table. Note that there can be multiple records with the same accession number.

chrom

The chromosome number that the gene impacted by the aberration is located on (No description available)

hgnc_gene

The HUGO Gene Nomenclature Committee (HGNC)-approved name for the gene impacted by the aberration (No description available)

id

Primary Key for aberrations table (No description available)

is_selected_aberration_flag

Flag indicating if the aberration record is a “selected aberration” (id is in the selected_aberrations staging table).

person_id

Person_id as corresponds to the OMOP dataset

stanford_aa_change

Amino acid (AA) change as reported in the Stanford STAMP results report. First letter indicates the amino acid impacted, indicated by its one-letter code, then a series of numbers which indicate the position of the amino acid within the protein sequence, then a string abbreviation which denotes the type of mutation (example - G646fs is a frameshift mutation occurring at the amino acid Glycine, position 646 within the protein sequence for the protein encoded by the impacted ASXL1 gene). (No description available)

stanford_break_1

No description available. This field is not well-populated.

stanford_break_2

No description available. This field is not well-populated.

stanford_gene

Gene impacted by the aberration, as reported in the Stanford STAMP results report. (No description available)

stanford_hgvs_coding

Standardized HGVS nomenclature representation for the variants in the coding DNA sequence of a gene, as reported in the Stanford STAMP results report (No description available)

stanford_hgvs_genomic

Standardized HGVS nomenclature representation for the variants in the genomic sequence of a chromosome, as reported in the Stanford STAMP results report (No description available)

stanford_hgvs_protein

Standardized HGVS nomenclature representation for the variants in the protein sequence, as reported in the Stanford STAMP results report (No description available)

stanford_interpretation

Text field containing interpretation of the aberration found, as reported in the Stanford STAMP results report (No description available)

stanford_minimum_copies

No description available. This field is not well-populated.

stanford_pathogenicity

Pathogenicity level of the aberration (No description available)

stanford_patient_uid

Internal Stanford tracking ID (this is the patient’s MRN | DOB)

stanford_region_1

No description available. This field is not well-populated.

stanford_transcript

No description available.

stanford_vaf

Variant allele frequency (VAF), as reported in the Stanford STAMP results report (No description available)

stanford_variant

Full variant the aberration causes, as reported in the Stanford STAMP results report (No description available)