A
web-based Atlas of Patient-Derived Xenografts
of cancer patients:A resource of MURAL PDX data
PDX model details
| PDX ID | 407M Cx |
|---|---|
| Host Strain(and Source) | NSG Source: Monash University |
| Host Strain Immune system Humanized | NO |
| Host Type | Castrate |
| Graft Site | Subcutaneous |
| Current Generation (* indicates number of generations grown in Castrate host) |
9 (5*) |
| Average PDX Generation Time (days +/- SEM) | 128 ± 30 |
| Tumor preparation | Tumor solid |
| Tumor Characterization Technology | Histology, IHC, STR profiling, targeted DNA sequencing, RNAseq |
| Tumor confirmed not to be of Mouse/EBV origin | Yes; negative for CD45 and/or positive for human CK8/18 and/or human mitochondria by IHC |
| Passage QA performed | Routine QA every 2-3 passages |
| Associated meta data | |
| PDX model availability | Yes (fixed, frozen or cryopreserved tissue) |
| Governance restriction for distribution | Available to investigators with appropriate ethics approvals, approved EOI from MURAL committee, and material transfer agreements |
| Pubmed ID | 34413304 |
| Markers | 407M Cx |
|---|---|
| AR | Y |
| PSA | Y |
| PSMA | Y |
| NE | N |
| ERG | N |
This table displays curated CNVs
| PDX ID | Gene Symbol | CNV Log2 | CNV Copy | CNV Call | Experiments name | Platform | Reference genome |
|---|---|---|---|---|---|---|---|
| 407M Cx | JAK1 | -0.885067 | 1.08292 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | SETD2 | -1.06766 | 0.954184 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | CHD1 | -0.994875 | 1.00356 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | APC | -0.994875 | 1.00356 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | IGF2R | -0.862998 | 1.09962 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | CDKN2A | -0.848417 | 1.11079 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | RB1 | -1.99062 | 0.503261 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | TP53 | -1.01445 | 0.990034 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | NCOR1 | -1.01445 | 0.990034 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | SMAD2 | -0.871669 | 1.09303 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | MBD1 | -0.871669 | 1.09303 | loss | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | GEMIN5 | 0.561987 | 2.9526 | gain | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | CHD7 | 1.86914 | 7.30629 | gain | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | MYC | 1.65733 | 6.30864 | gain | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | AKT1 | 0.944023 | 3.84777 | gain | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
| 407M Cx | KDM6A | 1.46993 | 2.77008 | gain | MURAL Prostate Cancer PDX collection | Targeted Twist Panel | hg19 |
Clinical Information
| Sample Number | 407M |
|---|---|
| Sample Site | Liver |
| Sample source | Biopsy |
| Pathology Tumor Diagnosis | None |
| Gleason Score | None |
| Primary Gleason Score | None |
| Secondary Gleason Score | None |
| Tertiary Gleason Score | None |
| ISUP Grade Group | |
| Tumor Grade | |
| D'Amico Risk Classification | |
| Tumor Volume (in cc) | 0.0 |
| Treatment Prior to Specimen Collection | ADT, docetaxel, abiraterone, enzalutamide |
Patient Information
| Patient Number | 407 |
|---|---|
| Sex | Male |
| Diagnosis | Prostate Cancer |
| PSA at diagnosis (ng/mL) | NA |
| Consent to share data | |
| Patient Tumor Collection (Current Model) | |
|---|---|
| Tumour sample ID | 407M |
| Patient Age (binned in 5 year age groups) | 75-79 |
This table displays curated sequence variants
The table can be sorted by any field. However, please note that when you click on a column header to sort, there might be a brief delay
The table can be sorted by any field. However, please note that when you click on a column header to sort, there might be a brief delay
| PDX ID | Gene Symbol | Depth | ALT_FREQ | Consequence | Exon | GnomAD_AF | CADD_PHRED | Clinvar_clnsig | Platform | Experiments Name | Reference | Library Type | Instrument Type |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 407M Cx | SMAD2 | 230 | 1.0 | stop_gained | '11/11 | . | 42 | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | TP53 | 226 | 1.0 | stop_gained | '4/11 | . | 35 | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | APC | 196 | 0.95 | frameshift_variant | '16/16 | . | . | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | AKT1 | 645 | 0.7 | missense_variant,splice_region_variant | '2/13 | 4.08E-06 | 25.9 | Pathogenic/Likely_pathogenic | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | MAST4 | 529 | 0.46 | missense_variant | '2/29 | 0.0008207 | 33 | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | NF1 | 228 | 0.39 | missense_variant | '51/58 | 0.0007889 | 25.4 | Conflicting_interpretations_of_pathogenicity | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | NOTCH3 | 384 | 0.31 | missense_variant | '6/33 | 0.0003093 | 24.7 | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | FOXO3 | 160 | 0.29 | frameshift_variant | '2/3 | 0 | 34 | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
| 407M Cx | CACNA1H | 540 | 0.26 | missense_variant | '10/35 | 0.0002622 | 4.878 | - | Targeted Twist Panel | MURAL Prostate Cancer PDX collection | hg19 | paired | NextSeq 500 |
No information in Gene expression
No information in Drug dosing Table