BackgroundFamilial adenomatous polyposis (FAP) is an autosomal dominant hereditary syndrome characterised by the development of hundreds to thousands of adenomatous colonic polyps during the second decade of life. FAP is caused by germ line mutations in the adenomatous polyposis coli (APC) gene located on chromosome 5q21–22.Case presentationA 36-year-old female was presented with 100–1000 adenomatous colonic polyps, typical of classic FAP symptoms. Genetic testing using massively parallel sequencing identified a 5-bp deletion (c.3927_3931delAAAGA) which causes frameshift (p.Glu1309Aspfs) and creates a premature stop codon, resulting in the replacement of the last 1535 amino acids of APC by five incorrect amino acids. Two of the proband’s four siblings also exhibited classic FAP symptoms and carried the same 5-bp heterozygous deletion in the APC gene. One of the proband’s two nephews also tested positive for this mutation but has not been examined by endoscopy due to his young age.ConclusionsWe reported here for the first time the use of massively parallel sequencing (MPS)-based genetic testing to identify a germline mutation within a three-generation Vietnamese family. This mutation is most likely responsible for the development of FAP.

54 Background: Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer and leading cause of cancer related death worldwide. Acquired genetic alterations in major driver genes including EGFR, KRAS, NRAS, BRAF, ALK and ROS1 are the most common mutations in NSCLC and certain mutations are associated with drug sensitivity or resistance. Hence, the mutation profiles of NSCLC patients are vital to guide targeted therapy and monitor the tumor recurrence, thereby improving the survival rate. The latest Globocan data showed that lung cancer ranks as the second most common cancer in Vietnam with high incidence and mortality rate. Nonetheless, the mutation spectrum of Vietnamese NSCLC patients has not been profiled thoroughly and current views on mutation testing largely rely on data obtained from previous prospective studies in Caucasian or East Asian cohorts. Methods: Massive parallel sequencing was employed to detect both somatic point mutations and rearrangement in six major driver genes in tissue biopsies from 350 NSCLC patients in Vietnam. The χ2/Fisher’s exact test was performed to compare mutation frequency between different cohorts. Additionally, both univariate and multivariate tests were used to identify clinical factors associated with mutation prevalence. Results: EGFR (32.3%) and KRAS (20%) accounted for the most frequently mutated genes, followed by ALK (5.4%), ROS1 (2.9%), BRAF (1.1%) and NRAS (0.6%). Our data showed a unique pattern of mutation profiles in Vietnamese NSCLC patients, with significant enrichment of KRAS mutation as compared to reported East Asian cohorts (20% versus 8%-10%, p < 0.05). Furthermore, EGFR and KRAS mutation frequencies were significantly associated with patients’ gender, with EGFR mutations more commonly detected in female than in male (48.1% versus 26.9%, p < 0.00001) while higher KRAS mutation frequency in male than in female (30.7% versus 9.2%, p < 0.0001). Young patients aged below the median age of 61 years had significantly higher tendency to acquire rearrangements in ALK (p = 0.02) and ROS1 (p = 0.03) than elderly patients. Conclusions: To our knowledge, our study is the first to reveal the mutation profiles of major druggable genes in a large cohort of Vietnamese NSCLC patients.

55 Background: The identification and quantification of actionable mutations are of critical importance for effective genotype-directed therapies, prognosis and drug response monitoring in patients with non-small-cell lung cancer (NSCLC). Although tumor tissue biopsy remains the gold standard for diagnosis of NSCLC, the analysis of plasma circulating tumor DNA (ctDNA), known as liquid biopsy, has recently emerged as an alternative and noninvasive approach for exploring tumor genetic constitution. In this study, we developed a mutation detection approach for liquid biopsy using ultra-deep massively parallel sequencing (MPS) with unique molecular identifier (UID) tagging and evaluated its performance for the identification and quantification of tumor-derived mutations from plasma of patients with advanced NSCLC. Methods: Tissue biopsy and plasma samples were collected from a total of 58 patients diagnosed with NSCLC in Vietnam. Genetic alterations in four driver genes including EGFR, KRAS, NRAS and BRAF were identified by using ultra-deep MPS combined with UID tagging. Subsequently, the concordance rate of mutation testing between matched plasma and tissue samples was assessed. Additionally, a commercially available ddPCR (Bio-rad) assay was used to conduct a cross-platform comparison with ultra-deep MPS for the detection and quantification of the three most common actionable EGFR mutations (del19, L858R and T790M). Results: Compared to the mutations detected in paired tissue samples, the plasma based ultra-deep MPS achieved high concordance rate of 87.5%. Cross-platform comparison with droplet digital PCR demonstrated comparable detection performance (91.4% concordance, Cohen's kappa coefficient of 0.85 with 95% CI = 0.72 – 0.97) and great reliability in quantification of mutation allele frequency (Intraclass correlation coefficient of 0.96 with 95% CI = 0.90 – 0.98). Conclusions: Our results highlight the potential application of liquid biopsy using ultra-deep MPS as a routine assay in clinical practice for both detection and quantification of actionable mutation landscape in NSCLC patients.

58 Background: Lung cancer is by far the leading cause of cancer death worldwide, with non-small cell lung cancer (NSCLC) accounting for the majority of cases. Genotype-directed therapy becomes a promising method for cancer treatment beside surgery and chemo-radiotherapy. Liquid biopsy using massive parallel sequencing has emerged as a non-invasive alternative procedure in profiling cancer driver mutations. In this study, we report the spectrum of clinically actionable mutations in plasma circulating tumor DNA of 299 non-small cell lung cancer patients using ultra-deep massive parallel sequencing with unique identifier tagging. Methods: Plasma circulating tumor DNA was extracted, ligated with unique identifier (Swift Bioscience), enriched of the target coding regions of EGFR, KRAS, NRAS, BRAF and the breakpoints of ALK, ROS1 (IDT) and sequenced using NextSeq 550 (Illumina) at mean coverage depth of 20,000X. Results: Out of 299 patients tested, 128 (42,8%) carried driver mutations. Genetic alterations were identified in EGFR (79 samples, 26,4%), KRAS (30 samples, 10%), ALK (7 samples, 2,34%), ROS1 (6 samples, 2%), BRAF (3 samples, 1%). There was no sample with NRAS mutation. In 79 EGFR-cases, there were 23 carry two pathogenic variants. 28 mutation types of EGFR were found including 19 indels and 9 missense variants L858R and T790M were the major ones. One case was found with concomitant EGFR and BRAF. Our study showed the spectrum and frequency of the cancer driver mutations detected in liquid biopsy was correlated to those detected in tissue biopsy samples. Conclusions: For the first time the spectrum of mutation types in liquid biopsy of Vietnamese NSCLC patients were investigated and showed the correlation with those detected in tissue biopsy samples.