InPreD sample ID nomenclature¶
InPreD sample IDs should be recorded with 19 characters, in format PPPyyyy-Ann-Bpq-Cll, where:
PPP is a three-letter project name (IPD in case of the current Oslo InPreD project);
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 type code:
D: DNA;
R: RNA;
C: cell-free samples;
nn is a two-digit assay type code:
01: TSO500 DNA assay;
03: TSO500 RNA assay;
50: Twist Human Core Exome Plus kit (DNA);
51: TruSeq Stranded mRNA kit;
B is a single-letter sample type code:
N: normal/control;
P: primary tumor, naive;
p: primary tumor, post-treatment;
R: regional metastasis, naive;
r: regional metastasis, post-treatment;
D: distal metastasis, naive;
d: distal metastasis, post-treatment;
C: cell-line;
L: liquid;
T: tumor [deprecated];
M: metastasis [deprecated];
p is the (n-1)th library preparation attempt:
0: first try;
1: second try (e.g., after cleaning, new extraction);
2: third try (ex: cleaning, new extraction++);
…
q is the nth biological replicate (e.g., using a different block or stock):
1
2
…
C is a single-letter code for sample material:
A: archived (FFPE);
B: blood;
C: cytology;
F: fresh frozen;
ll is a two-digit code for tumor site (these codes are adopted from PCGR):
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.
X can be used to replace any missing (yet unknown) information.