OSPL "out the pipe"
OSPL Biomarkers
OVPL not-biomarkers
OVPL Biomarkers and Intersting Stuff
Guess who?
100

Designation of whether the biopsy specimen was taken from a known metastasis

localMet

100

Cosmic's Original 7.

ClassicSignature

100

FMI’s assignment of disease type, disease that gets matched to disease tree.

diseaseOntology

100

Amino acid change.

proteinEffect_SV or reannotProteinEffect_SV

100

Result of “The classifier is trained on 1000 Genomes data”

ancestryCall

200
  • A value of ‘-999’ is used whenever there is a copy number override
  • - A value of ‘-998’ is used whenever the is insufficiently able to distinguish from noise in the data
  • - A value of ‘-404’ is used when contamination is present and there is no candidate variant ≥ 5x the contamination level. 
  • - A value of ‘-1’ is used when script errors out

cTFvalue

200

HRD “score.”

percentGenomeLoh

200

One of the available columns for this category is named after a beloved fictional droid.

baitSet

200

‘MET_ex_14’
‘EGFR_ex_19_del’
‘EGFR_ex_19_ins’
‘EGFR_ex_20_ins’
‘ERBB2_ex_20_ins’ ‘FLT3_ITD’

specialAnnotations

200

The laboratory which performed PD-L1/PD-1 staining.

path_lab

300

Diagnosis listed on test order form.

pathologyDiagnosis

300

30 of them.


ExpandedSignature

300

True or False for whether a variant can be detected on a baitset – hint, we're discussing splitting this column due to the unique nature of this baitset.

AB1_captured

300

Named for neither the prestigious science fiction literary award, nor the 2011 Martin Scorsese Adventure film—nor weavings.

geneHugo

300

Returned from NCBI Blast

pathogenName

400

**None if a CF2 or CF3 sample or sample was processed October 24th-28th, 2018** 

float 0 - inf 

**‘None’ for samples processed between 24-28 October 2018* 

rawTMBscore

400

Available on a subset of DX1-tested samples only.

hlaLohStatusImputed.

400

Which types of variants have variant IDs variantID corresponding to 6XXXXXXX

NonHumanVariants.

400

Can be None, NA, and another negative-sounding value, but this last one is “not” bereft of communicating information.

zygosity_SV

400

What is OPPL "score" exactly

The percentage of relevant cells staining for the marker.

                                                       


    

500

# of coding short variants either called as “probable germline” or are present in dbSNP

SGZsample

500

Name “biomarkers 1 – 5” perfectly for me.

lunch and breakfast

500

Which types of variants have variant IDs variantID corresponding to 4XXXXXXX

substitution SVs from the *substitutions.txt file

500

This column exists in the build but is pending implementation. Will compare the frequency of variant identification in two different cohorts of samples.

MSIrate_SV

500

2nd smallest oscillating copynumber posterior probability, Poisson Dist., (λ= 2.627145279)

osCN2

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