Table 1 Internal clinical genomics data model for genetic test result curation

Hugo_Symbol

Gene Symbol

String

EGFR

75% for Positive, 20.8% for VUS

Ensemble_Gene_ID

Ensemble Gene ID

String starting with prefix "ENSG"

ENSG00000146648

0%

Transcript_ID

Transcript ID

String starting with prefix "NM" or "NR"

ENSG00000146648

0%

De_sample_ID

De-identified sample ID

String

MCM123

-

Pathogeneity_Report_Date

Date of initial genetic report

String of mm/dd/yyyy

2/12/2006

0%

Variant_Type

Type of variants

String of "SNP", "INDEL", “CNV”, “Rearrangement”

SNP

50%

Variant_Source

Somatic or germline

String of "somatic" or "germline"

germline

26.4%

Variant_Pathogenicity

Initial reported pathogenicity

String of "actionable", "pathogenic", or "VUS"

pathogenic

43.8%

Variant_Classification

Selected strings from some of below:

Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site, Translation_Start_Site, Nonstop_Mutation, 3′UTR, 3′Flank, 5′UTR, 5′Flank, IGR, Intron, RNA, Targeted_Region, De_novo_Start_InFrame, De_novo_Start_OutOfFrame

Missense_Mutation

6.3%

HGVS_Short

HGVS nomenclature for cDNA and Amino Acid Change

A string following HGVS nomenclature to detonate protein amino acid change

p.Arg149Trp

25%

NCBI_Build

The Genome Reference Consortium Build

"GRCh37"

0%

Chromosome

Chromosome of event

String of "1"-"22", "X", "Y", "M"

"7"

0%

Start_Position

Start position of event

Numerical

0%

End_Position

End position of event

Numerical

0%

Strand

Strand that the mutation is reported for

Character of "+" or "−"

"+"

0%

Variant_Allele_Freq

Percentage of variant presence in the sample

Numerical between 0 and 100

30

0%

BP_Coverage

Base-pair coverage

Numerical

270

0%

Variant_Pathogenicity_Updated

Updated pathogenicity

-

Pathogeneity_Update_Date

Update date

-