1. Cancer validation meeting

2. RMH Case Clinical History (47year old female)
Diagnosis
Disease cohort: Renal
Subtype: Unknown
Diagnosed July 2016
G3 pT2b; pN0; pMx (TNM 7th edition)
7th Edition)
Previous molecular testing
Germline: Known p53 germ line carrier Li Fraumeni syndrome (C>T codon 196, premature stop)
No routine somatic testing performed in renal cases
Young son; tested for p53 germ line mutation-confirmed mutation (under care of GOS)
History
Complex clinical history; prophylactic double mastectomy (2000), right oopherectomy (2007), several benign moles and cervical biopsy (benign)
Participant in SIGNIFY study-use of whole body MRI to screen patients with rare p53 germline mutations
11cm renal mass was identified plus a uterine fibroid
Treatment
Nephrectomy/hysterectomy/unilateral salpingoophorectomy/utererolysis
Follow-up
MRI imaging-admitted with left sided weakness and vertigo Dec 2016
Brain lesion observed; histology confirmed high grade glioma-new primary and not metastasis from RCC
Referred for phase 1 trials; debulking of posterior fossa glioblastoma multiforme-concomitant chemo-radiotherapy, completed 6 cycles of temozolomide; recurrent disease-commenced second line PVC chemotherapy
No further treatment options at time of tumour board review due to declining PS; sadly she has since passed away
Most Diagnosis based on immunophenotyping, morphology aspirate/trephine and histo/IHC;
Subtypes/sub-classifications based on molecular results and also prognostic information which will be reflected in therapy choices
Minimal residual disease monitoring (MRD)

3. Results Technical aspects of sequencing Tumour content % : 50
Pathology CPD club
Results
Technical aspects of sequencing
Tumour content % : 50
Genome wide coverage mean 92X
Total somatic SNVs 16645, total somatic indels 21680, total SVs
Domain 1
None
Domain 2
SMAD2
SMAD Family Member 2
c.1109A>G p.(Gln370Arg) 55% VAF
SMAD proteins are signal transducers and transcriptional modulators that mediate multiple signaling pathways. This protein mediates the signal of the transforming growth factor (TGF)-beta, and thus regulates multiple cellular processes, such as cell proliferation, apoptosis, and differentiation.

4. Results RAD21 RAD21 Cohesin Complex Component
Pathology CPD club
Results
RAD21
RAD21 Cohesin Complex Component
c.815-5delT 25% VAF (12/48)-quite a noisy region and adjacent to regions of homopolymers
• This protein is a nuclear phospho-protein, which becomes hyperphosphorylated in cell cycle M phase. The highly regulated association of this protein with mitotic chromatin specifically at the centromere region suggests its role in sister chromatid cohesion in mitotic cells.
NUTM2B
NUT Family Member 2B
c.925A>G p.(Ser309Gly) 34% VAF (13/38)
NUTM2B (NUT Family Member 2B) is a Protein Coding gene. Diseases associated with NUTM2B include Kidney Clear Cell Sarcoma and Endometrial Stromal Sarcoma.
LYL1, Basic Helix-Loop-Helix Family Member
c.718G>A p.(Gly240Arg) 39% VAF (20/51)
Represents a basic helix-loop-helix transcription factor. The encoded protein may play roles in blood vessel maturation and hematopoeisis.
A translocation between this locus and the T cell receptor beta locus (GeneID 6957) on chromosome 7 has been associated with acute lymphoblastic leukemia.

5. Results and summary Domain 3
Pathology CPD club
Results and summary
Domain 3
Available in supplementary report (not reviewed)
Pertinent Germline findings
No reported in line with disease setting
Discussed with GEL the know p53 germ line status
confirmed a TP53 variant was detected in this patient’s germline vcf.
NM_ (TP53):c.586C>T (p.Arg196Ter)
No actionable variants detected (no domain 1 variants)
Her son is being monitored as confirmed p53 carrier

6. Pertinent germ line findings
Pathology CPD club
Pertinent germ line findings
Tumour Type
Genes analysed
Breast cancer
BRCA1, BRCA2, PALB2, PTEN, TP53
Colorectal cancer
MLH1, MSH2, MSH6, MUTYH (bi), PMS2, POLD1, POLE, PTEN, SMAD4, STK11
Ovarian cancer
BRCA1, BRCA2, MLH1, MSH2, MSH6, BRIP1, RAD51C, RAD51D
Prostate cancer
BRCA2
Renal Cancer
FH, FLCN, PTEN, SDHB, VHL, MET
Sarcoma
TP53
Melanoma
BAP1, (CDK4), CDKN2A
Endometrial cancer
FH, MLH1, MSH2, MSH6, PMS2, PTEN
Adult Glioma
APC, ATM (bi), MLH1, MSH2, MSH6, PMS2, TP53
Upper GI
MLH1, MSH2, MSH6, PMS2
Head and Neck
BRIP1 FANCA FANCB FANCC FANCD2
FANCE FANCF FANCG FANCI FANCL FANCM
Neuroendocrine
CDKN1B, MAX, MEN1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, TMEM127, FH, VHL

7. RMH Case Clinical History (58year old female)
Diagnosis
Clear cell adenocarcinoma of the ovary. Stage3A1. Involved pelvic lymph node (1/4).
CA125 73
No pathogenic BRCA1/2 mutations identified
: Underwent laparotomy; radical abdominal hysterectomy, bilateral salpingoophorectomy, bilateral pelvic node dissection, infracolic and infragastric omentectomy
No residual disease
Oct 2016-Feb 2017: Adjuvant chemo with Carboplatin/Paclitaxel 6 cycles due to rare & aggressive subtype
Progression
Follow-up scan in June 2017 showed disease progression to liver; platinum resistance
Entered onto NICCC trial: randomised to Pegylated Liposomal Doxorubicin (caelyx)
Progression after two cycles of Caelyx (liver and peritoneal disease)
Referral to Drug Development Unit (DDU): Consented for GenambAXL trial (phase 1 trial)
Rapid progression on trial - palative
Died
Most Diagnosis based on immunophenotyping, morphology aspirate/trephine and histo/IHC;
Subtypes/sub-classifications based on molecular results and also prognostic information which will be reflected in therapy choices
Minimal residual disease monitoring (MRD)

8. GEL report
Date issued

9. SNVs All three SNVs confirmed by second NGS panel Variant
GEL WGS (VAF%)
Mean coverage 96x
RMH Ovarian (VAF%)
Minimum depth 80x (99.7%)
Capture panel
ATM
c.5644C>T p.(Arg1882*) stop gained
68 (58/85reads)
75 (468/632reads)
PIK3CA
c.3140A>T p.(His1047Leu)
44 (59/133reads)
40 (245/622reads)
ARID1A
c.6150G>A p.(Trp2050*)
87 (82/94reads)
81 (459/575reads)

10. CNV Variant GEL WGS (VAF%) RMH Ovarian (VAF%) % Gene >2.40 = 79%
Mean coverage 96x
RMH Ovarian (VAF%)
Minimum depth 80x (99.7%)
Capture panel
CDKN2A/CDKN2B amplification
chr9:  
low confidence gain. variant was called but did not pass filters
% Gene >2.40 = 79%
ROI 11/14
SMARCA4 deletion
chr19:
high confidence LOH
% Gene <0.5 = 9%
ROI 3/35
MAP2K2
Not confirmed
% Gene <0.5 = 10%
ROI 1/10

11. CDKN2A/B amplification

12. MAP2K2 and SMARCA4 deletion