Liquid BIOpsy for MiNimal RESidual DiSease Detection in Head and Neck Squamous Cell Carcinoma (LIONESS)—a personalised circulating tumour DNA analysis in head and neck squamous cell carcinoma
2022.02 BJC (IF = 7.6)
Inivata
Methods
- personalised assay using deep sequencing of up to 48 primer pairs
- multiplex PCR and targeted NGS.
- PCR, with a median value of 14,550 copies.
- combined with a fixed primer panel of 21 common population-specific SNPs for quality control purposes during the NGS testing
- at least one somatic vars
- the removal of variants due to clonal haematopoiesis of indeterminate potential (CHIP)
- a statistical model was used to assess the statistical significance of the observed mutant counts
- an assessment of the noise of each individual variant class and the sensitivity and specificity based on the number of variants in the panel.
- A sample will be called as positive for residual disease if its cumulative statistical score is above a pre-set threshold, as defined during analytical development.
- The tumour fraction estimated from this model was then reported (estimated variant allele frequency, eVAF).
Study design
- LIONESS is a single-centre non-interventional prospective experimental evidence-generating cohort study
- Stages III-IVb
- Patients with distant metastasis (cM1) or other active malignancies at the time of enrolment were excluded.
- The primary objective was the early identification of patients with minimal residual disease post-operatively and/or molecular-level disease recurrence within 6 months of follow-up with outcome measure determined as presence of ctDNA in plasma of patients with HNSCC.
→ ctDNA was detected (red circle)
→ not detected (black circle)
→ subsequently relapsed (inverted yellow triangle)
→ dashed line : total duration of follow-up for each patient
→ followed up for a median duration of 371 days (292–532 days)
→ blue line indicates the lead time which is the interval between the first ctDNA-positive post-surgery sample and clinical confirmation of disease recurrence.
ctDNA Detection
→ Stage IV (laryngeal tumour), Stage I (mouth tumour)
→ 47,35 Vars
→ No adjuvant treatment for Stage IVa disease was possible because of radiation doses the patient had received in the past
→ Stage I ND.
→ Importantly, the increase in ctDNA preceded the local recurrence confirmed by panendoscopy and biopsy of the neopharynx 108 days later.
→ Stage III
→ 43 vars
→ the patient declined adjuvant radiotherapy for Stage III
→ resection margins were clear (≥5 mm)
→ potential of personalised ctDNA monitoring for further treatment decisions as disseminated tumour cells may have caused the post-operative ctDNA detection.
→ Stage III, no mets
→ 10 somatic vars
→ due to a high number of germline variants or variants that were absent in the primary tumour DNA at panel quality control
→ decreased immediately after surgery to undetectable levels
→ local recurrence (resected)
→ early increase in ctDNA post-operatively and prior to adjuvant therapy suggests minimal residual disease
→ may have allowed surgeons to consider additional resection or adj. therapy in 122 days
→ Stage IV
→ 40 vars
→ no samples could be collected immediately after the completion of adjuvant therapy
→ impossible to say whether ctDNA levels remained elevated throughout the adjuvant treatment, or whether there had been a drop after adjuvant radiochemotherapy
→ the surge in ctDNA suggested the occurrence of a metastasis ( lung, bone, confirmed by scans afterwards )
→ Stage III
→ 46 vars
→ ctDNA levels showed a subsequent increase to 0.0064% VAF around one month after completion of adjuvant treatment.
→ the disease was deemed unresectable, primarily because the patient did not qualify for radical surgery and reconstructive measures needed due to extensive comorbidities(2+ diseases at the same time).
Spec
- Exome→ Mean Cov. 100-300
- → up to 52 vars
- LoD
- Using NA12878
Discussion
- Previous study 에서 암종별 ctDNA(+) %→ 92% with Stages III and IV
- → ~70% of patients with metastatic HNSCC
- → 70% of patients with HNSCC Stage I and II
- higher levels of ctDNA were detected in patients with clinical N2-N3 disease compared to patients with clinical N0-N1 disease
- able to detect pre-operative ctDNA in 100% of patients. (mainly late stage)
- detected prior to progression, with lead times ranging from 108 to 253 days.
- Confirmation of post-operative tumour clearance by undetectable ctDNA could potentially allow a more flexible start of additional therapeutic measures
- positive post-operative ctDNA or an increase of ctDNA levels soon after tumour resection may indicate minimal residual disease independently from intra-operative analysis of frozen sections.→ particularly in cases where adjuvant treatment will not be possible or plan further surgeries accordingly
- → the operating surgeon may consider additional resection
- rising ctDNA levels prior to start of adjuvant treatment may trigger re-assessment of distant lesions initially deemed non-suspicious in pre-operative imaging
- evaluation of ambiguous radiological findings may also be aided by personalised ctDNA analysis
— limitations —
- ctDNA detection is reported at the sample level, giving a high degree of sensitivity, but does not inform on the levels and tracking of individual variants or the emergence of sub-clones.
- Our personalised ctDNA assay design requires suitable FFPE tumour material to be available for WES, which may not always be achievable and may limit the use of this method in certain specific cases
- increasing number of patients would not have suitable numbers of variants and it would increase the risk of assay failure due to primer multiplexing
댓글