InPreD sample ID nomenclature

(v.4, March 17 2025)

InPreD sample IDs should be recorded with 19 characters, in format PPPyyyy-Ann-Sxz-Mll, where:

  • PPP is a three-letter Project code:

    • IPA: InPreD AHUS;

    • IPD: InPreD OUS;

    • IPH: InPreD HUS;

    • IPO: InPreD St. Olav;

  • yyyy is a four-digit patient code (all samples of a given patient should have the same patient code within a specific project);

  • A is a single-letter nucleic acid input type code:

    • C: Cell-free samples;

    • D: DNA;

    • R: RNA;

  • nn is a two-digit assay type code:

    • 01: TSO500 DNA;

    • 02: Archer FusionPlex Lung assay;

    • 03: TSO500 RNA;

    • 04: EPIC DNA methylation;

    • 05: whole-genome DNA sequencing (WGS);

    • 06: TSO500 HRD (TSO500 solid + HRD);

    • 07: whole-transcriptome RNA sequencing (WTS);

    • 50: [external] Twist Human Core Exome Plus (DNA);

    • 51: [external] TruSeq Stranded mRNA;

  • S is a single-letter sample type code:

    • A: post Allotransplantation;

    • C: Cell-line;

    • D: Distal metastasis, naive;

    • d: distal metastasis, post-treatment;

    • E: naive;

    • e: post treatment;

    • L: Liquid;

    • M: Metastasis;

    • N: Normal/control;

    • P: Primary tumor, naive;

    • p: primary tumor, post-treatment;

    • R: Regional metastasis, naive;

    • r: regional metastasis, post-treatment;

    • T: Primary tumor;

    • X: unknown;

  • x is the (n-1)th library preparation attempt:

    • 0: first try;

    • 1: second try (e.g., after cleaning, new extraction);

    • 2: third try;

    • …

    • 9: validation/verification test;

  • z is the nth biological replicate (e.g., using a different block or stock):

    • 1

    • 2

    • …

  • M is a single-letter code for sample material:

    • A: Archived (FFPE);

    • B: Blood;

    • C: Cytology;

    • E: Extramedullary;

    • F: fresh Frozen;

    • M: fresh bone Marrow;

    • S: buccal Swab;

    • X: unknown.

  • ll is a two-digit code for tumor site (these codes are adopted from PCGR):

    • 00: Cancer origo incerta;

    • 01: Adrenal Gland;

    • 02: Ampulla of Vater;

    • 03: Biliary Tract;

    • 04: Bladder/Urinary Tract;

    • 05: Bone;

    • 06: Breast;

    • 07: Cervix;

    • 08: CNS/Brain;

    • 09: Colon/Rectum;

    • 10: Esophagus/Stomach;

    • 11: Eye;

    • 12: Head and Neck;

    • 13: Kidney;

    • 14: Liver;

    • 15: Lung;

    • 16: Lymphoid;

    • 17: Myeloid;

    • 18: Ovary/Fallopian Tube;

    • 19: Pancreas;

    • 20: Peripheral Nervous System;

    • 21: Peritoneum;

    • 22: Pleura;

    • 23: Prostate;

    • 24: Skin;

    • 25: Soft Tissue;

    • 26: Testis;

    • 27: Thymus;

    • 28: Thyroid;

    • 29: Uterus;

    • 30: Vulva/Vagina;

    • XX: unknown.

(last updated: 2025-03-17)