Annual Meeting Proceedings Part 1 - American Society of Clinical ...

662s Tumor Biology
10524 Poster Discussion Session (Board #17), Tue, 8:00 AM-12:00 PM and
11:30 AM-12:30 PM
Next-generation sequencing of FFPE solid tumor specimens for clinical
use. Presenting Author: Roman Yelensky, Foundation Medicine, Cambridge,
MA
Background: As more therapies targeting genomic alterations become
available, genotyping (e.g., by Sequenom) is increasingly performed in
tumor types where mutational status may drive treatment choice. Nextgeneration
sequencing (NGS) technology can expand on genotyping of
individual base pairs because it can detect mutations across entire exons,
copy changes and fusion genes. However, for NGS to be clinically viable, it
must be made compatible with FFPE tissues and shown concordant with
best current diagnostic methods. Methods: To explore a potential clinical
role for NGS, we selected 120 FFPE specimens (68 NSCLC, 32 CRC, 20
melanoma) previously tested for 97 oncogenic mutations in 8 oncogenes by
Sequenom, and sequenced all exons of 182 cancer genes. Genotyping and
sequencing were both performed in CLIA compliant labs. DNA was
extracted from 4x 10� unstained sections from the diagnostic FFPE block,
followed by library construction and hybridization capture of 3230 exons
and 37 commonly rearranged introns. Average coverage of �900X uniquelymapping
reads was obtained. Sequence data were analyzed for all genomic
alterations and examined for potentially actionable mutations. Results:
High concordance was noted between Sequenom and NGS: 103 and 105
mutations were called by the two technologies, respectively, at mutually
tested sites, with 97 mutation calls in common. Notably, mutant allele
frequencies in concordant calls ranged as low as 2% by NGS, highlighting
the sensitivity of detection enabled by both approaches. Furthermore, in
45/120 (38%) specimens, NGS revealed additional alterations that may
confer sensitivity or resistance to approved or experimental targeted
therapies and thus plausibly influence treatment decisions. These included
39 copy changes or loss-of-function variants best assayed by an NGS
approach. Conclusions: Our results demonstrate technical feasibility and
highlight potential benefits of comprehensive cancer gene characterization
through next-generation sequencing of clinical FFPE specimens. As NGS is
the most practical means to detect all classes of somatic alteration in a
small, clinically relevant sample, we suggest that this type of testing will
become an essential component of patient care.
10526 Poster Discussion Session (Board #19), Tue, 8:00 AM-12:00 PM and
11:30 AM-12:30 PM
Frequency and clinical characterization of NSCLC patients harboring
PIK3CA mutations identified within a regional screening network. Presenting
Author: Masyar Gardizi, Lung Cancer Group Cologne, Center for
Integrated Oncology, University Hospital Cologne, Cologne, Germany
Background: PIK3CA mutations are a rare oncogenic event of potential
therapeutic relevance in NSCLC. Here we report frequency and characteristics
of patients with PIK3CA mutated lung tumors. Methods: Patients with
NSCLC and PIK3CA mutations were identified within our regional Network
for Molecular Screening in Lung Cancer. We further analyzed the presence
of BRAF, KRAS, EGFR mutations as well as ALK translocation, ERBB2 and
FGFR1 amplifications in PIK3CA mutated samples. Clinical data on age,
sex, TNM classification and tumor stage, histological type, grading, overall
survival, smoking status, comorbidity, BMI and secondary malignancies
were retrieved from clinical charts in accordance with the local ethics
committee. Results: PIK3CA mutations were detected with a frequency of
3.7% (24% exon 20,76% exon 9) in 1000 patients. Histologically 32%
were defined as squamous cell carcinoma, 48% as adenocarcinoma and
18% other histological subtypes or NSCLC-NOS. Exon 9 mutations were
present in the acinar and lepidic subtype, whereas exon 20 mutations were
seen in the papillary and solid subtype. Cooccuring genetic lesions were
observed in 16% (mutations in KRAS�2, EGFR�1, BRAF�1; FGFR1
amplification�2). 14 were female, 23 male with a mean age of 69 years.
21 of these patients were further clinically annotated. 11 patients
presented with stage IIIb/IV eligible for palliative treatment and 10 stage I –
IIIa eligible for surgical therapy �/- adjuvant therapy. All but 1 patient were
smokers with an average BMI of 26,2kg/m2 with a typical high load of
comorbidity mainly of cardiovascular diseases, 8 of 21 patients showed
prior malignancies in their medical history. The median overall survival
within this population has not been reached yet. Conclusions: Screening for
PIK3CA mutations is feasible. A high proportion (38%) of patients with
PIK3CA mutated lung cancer have prior malignancies and show a high load
of comorbidity. Furthermore PIK3CA mutations are not exclusive to KRAS,
EGFR or BRAF mutations or FGFR1 amplifications. Successful identification
of patients with oncogenic lesions in lung cancer in a screening
network might allow future personalized treatment of these patients.
10525 Poster Discussion Session (Board #18), Tue, 8:00 AM-12:00 PM and
11:30 AM-12:30 PM
Prospective study of oncogenic mutations in circulating cell-free DNA
(cfDNA) using a multiplex sequencing platform for patient (pt) allocation to
phase I clinical trials. Presenting Author: Michael Ong, Royal Marsden
Hospital and Institute of Cancer Research, Sutton, United Kingdom
Background: Studies suggest that tumoral cfDNA can be isolated from
plasma and used as a biomarker. Methods: We conducted a prospective
study in adult pts with advanced cancer referred for phase I clinical trials
Sep09-Dec10 (A: Pilot Phase n�104) and Jan11-Sep11 (B: Expansion
Phase n�176). cfDNA and tumor DNA from formalin-fixed paraffinembedded
(FFPE) tissue were isolated, quantified, and analyzed for 238
mutations in 19 oncogenes by the Sequenom OncoCarta Panel 1.0.
Mutation data were used for trial allocation when available. Pt data and
outcomes were collected. Statistical inferences used Wilcoxon rank-sum
and Pearson’s Chi-squared. Results: 280 pts enrolled including breast (60),
colorectal (42), ovarian (37), lung (31), and prostate (20); median age
60yrs [23-81]; 93% ECOG PS 0-1. cfDNA in 95% and FFPE in 60% were
analyzed. Median time to cfDNA result, trial allocation and consent were 7
[5-14], 6 and 23 d. Median cancer pt cfDNA concentration (ng/ml) (A: 18
[1-1600]; B: 34 [16-1657]) was higher than 20 healthy volunteers (6
[5-13] A: p�0.0001) and higher in metastatic vs locally advanced cancer
(A: 21 vs 4 p�0.0006; B: 42 vs 24 p�0.066). Pts with higher than
median [cfDNA] had shorter median survival (MST) than below (A: 217 vs
274 d, HR 1.72 95% CI 1.07-2.65, p�0.025; B: MST not reached yet).
Mutations were found in 89 pts (32%), including KRAS (11%), PIK3CA
(5%), MET (5%), BRAF (4%), and AKT (2%). cfDNA mutations (57 pts,
21.5%) were mainly found above the median [cfDNA] (A: 41 vs 17%
�2�6.9, p�0.009; B: 24 vs 11% �2�5.0, p�0.025). Of 155 pts with
both cfDNA and FFPE available, 68 had mutations detected: 30 identical
in cfDNA and FFPE; 28 in FFPE alone and 10 in cfDNA alone. Overall, 153
pts were treated on a phase I trial; 23 pts had relevant mutation data and
received a trial targeting the PI3-Akt-mTOR axis. Conclusions: Higher
cfDNA is associated with greater disease burden, worse prognosis, and
higher mutation detection rate, suggesting cfDNA is tumorally derived.
Moreover, cfDNA can be analyzed for oncogenic mutations in a time-frame
suitable for clinical decision making, making it a potentially useful
non-invasive adjunct to tumour DNA analysis.
10527 Poster Discussion Session (Board #20), Tue, 8:00 AM-12:00 PM and
11:30 AM-12:30 PM
Association of EGFR mutation or ALK rearrangement with expression of
DNA repair and synthesis genes in never-smoker females with pulmonary
adenocarcinoma. Presenting Author: Xiaoxia Chen, Department of Oncology,
Shanghai Pulmonary Hospital, Tongji University; Tongji University
Medical School Cancer Institute, Shanghai, China
Background: Epidermal growth factor receptor (EGFR) mutation or anaplastic
lymphoma kinase (ALK) rearrangement was found not only predict the
efficacy of targeted drugs, but also associate with the efficacy of chemotherapy
drugs in non-small cell lung cancer (NSCLC) patients. We investigated
the relationship of EGFR mutation status or ALK rearrangement and
DNA repair or synthesis genes, such as excision repair cross-complementing
1 (ERCC1), ribonucleotide reductase subunit M1 (RRM1), thymidylate
synthetase (TS) and breast cancer gene one (BRCA1) gene expression, as a
potential explanation for these observations. Methods: In this surgical
series, 104 resected lung adenocarcinomas from nonsmoker females were
analyzed concurrently for the EGFR mutation, ALK rearrangement status
and mRNA expression of ERCC1, RRM1, TS and BRCA1 genes. EGFR
mutation detection was performed by the method of ADx-ARMS, ALK
rearrangement was detected by PCR and the mRNA expression of different
genes were tested using the method of real-time PCR. Results: 73 (70.2%)
patients harbored EGFR mutations and 10 (9.6%) had ALK rearrangement.
The ERCC1 mRNA level in patients with EGFR mutation was
3.44�1.94�10 -3
, which is significantly lower than in the patients with
ALK positive and both negative(4.60�1.95�10 -3 and 4.95�2.33�10 -3
respectively, P�0.010). While the TS mRNA levels were significantly lower
in the patients with EGFR mutation(1.15�1.38�10 -3 VS
2.69�3.97�10 -3 , P�0.006) or ALK positive (1.21�0.78�10 -3 VS
2.69�3.97�10 -3 , P�0.020) than in patients with both negative.
Conclusions: NSCLC specimens harboring activating EGFR mutations are
more likely to express low ERCC1 and TS mRNA levels, while NSCLC
patients with ALK rearrangement are more likely to express low TS mRNA
levels, which could be helpful to select a proper chemotherapy regimen for
NSCLC patients with known EGFR mutation or ALK fusion status.
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