Abstract 3991: ONCOTARGET (ONCOALVO): A custom NGS panel for therapeutic decision in solid tumors refractory to conventional therapy

Next-generation sequencing (NGS) of tumor biopsies of both solid tumors, as well as hematological malignancies, using commercially available platforms has broadly entered routine clinical practice in medical oncology. This molecular diagnostic approach is now used mainly to test for predictive biomarkers for patients with no available further standard therapies, as diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. However, the high cost of large multigenic panels and especially the sequencing of the entire tumor exome is a concern, especially in a developing country such as Brazil. Here we report the clinical application of a panel of 57 genes that we call ONCOTARGET (ONCOALVO) which is based on the Thermo Fisher Oncomine Focus Assay, an integrated, commercially available NGS assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance, but with 5 additional genes: the homologous recombination repair (HRR) genes BRCA1, BRCA2, ATM and CHEK2 that determine tumor sensitivity to inhibitors of the PARP enzyme and also KDR, which determines sensitivity to regorafenib. Twenty-five diagnostic samples of formalin-fixed, paraffin-embedded material submitted for molecular testing over a 8-month time period were analyzed so far. All patients had advanced solid tumors already refractory to conventional systemic therapy. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent S5 sequencer. Sequencing datasets were analyzed using the Ion Reporter software. From the samples of the 39 patients tested, we found 30 potential therapy target pathogenic gene aberrations in 22 (56.4%) patients: KRAS - 7 (23.3%), BRCA1 - 6 (20%), BRCA2 - 5 (16.6%), PIK3CA - 3 (10%), MAP2K1 - 2 (6.6%), BRAF-V600E - 2 (6.6%) mutations; and also one of each: ERBB2 (3.3%), mTOR (3.3%), KIT (3.3%), ALK (3.3%) mutations and one (3,3%) CCND1 amplification. In 3 (7,69%) patients there were double mutations: BRCA1 and BRCA2 in 2 cases and BRCA2 and KRAS and one case. The Oncotarget workflow enabled a turnaround of 18 frac12 days. Taken together, ONCOTARGET was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics and therapeutic decisions with a potential to become an important assay for precision oncology in Brazil.

Citation Format: Andre M. Murad, Jose Claudio Casali-da-Rocha, Juliana G. Carneiro, Ana L. Godard. ONCOTARGET (ONCOALVO): A custom NGS panel for therapeutic decision in solid tumors refractory to conventional therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3991.

DNA Base-Excision Repair Genes OGG1 and NTH1 in Brazilian Lung Cancer Patients

INTRODUCTION

Lung cancer is the leading global cause of cancer-related mortality and is associated with poor prognosis. To improve survival rates of lung cancer patients, better understanding of tumorigenic mechanisms is necessary, which may lead to development of new therapeutic strategies. The hOGG1 and NTH1 genes act in the DNA BER repair pathway and their involvement in lung cancer pathogenesis has been analyzed in several populations.

METHODS

We analyzed targeted regions of the hOGG1 and NTH1 genes in 96 Brazilian patients with non-small-cell lung cancer (NSCLC) and 89 cancer-free, ethnically matched controls.

RESULTS

The NTH1 c.98G>T polymorphism rs2302172 (p = 0.02 and p = 0.02 for allele and genotype frequency between cases and controls, respectively) and the 140-17C> T variant (rs2233518) (p = 0.02 and p = 0.02 for allele and genotype frequency between cases and controls, respectively) were detected in four lung cancer cases (4 %) while the NTH1 Q131K (C391A) polymorphism was found in seven lung cancer cases (7 %) (p = 0.001 and p = 0.008, for allele and genotype frequency between cases and controls, respectively). None of these sequence variants were detected in controls. The Ser326Cys (C1245G, rs1052133) polymorphism in the OGG1 gene was detected in 42 % of analyzed NSCLC patients and in 34 % of the controls (p = 0.11 and p = 0.25 for allele and genotype frequency between cases and controls, respectively).

CONCLUSIONS

Our study provides preliminary evidence that polymorphisms in OGG1 do not contribute to development of NSCLC in Brazilian patients and that NTH1 polymorphisms may be associated with NSCLC pathogenesis.

Influence of gender on the EMG signal of the quadriceps femoris muscles and performance in high-intensity short-term exercise

The aim of this study was to investigate the influence of gender on the EMG signal of the muscles of the quadriceps femoris and the physical performance in high-intensity, short-term exercise. Fourteen volunteers (7 men = 29.1 +/- 2.8 years and 7 women = 22.6 +/- 2.9 years) performed a Wingate Test (WT) with a load of 7.5% of body mass. The variables analyzed during the WT were the Relative Peak Power (W.Kg(-1)) (RPP), Relative Mean Power (W.Kg(-1)) (RMP), Fatigue Index (%) (FI) and Peak Power Instant (s) (PPI). EMG signals of the superficial muscles of the quadriceps femoris (QF) from the right leg: rectus femoris (RF), vastus lateralis (VL) and vastus medialis (VM) were analyzed through root mean square (RMS) values and the normalized median frequency (MNF) determined using the Fast Fourier Transform (FFT). The RPP and the RMP were significantly higher in men when compared to women (9.99 +/- 0.96 vs. 7.66 +/- 1.00 W.kg(-1); 7.23 +/- 0.49 vs. 5.65 +/- 0.61 W.kg(1), P < 0.05; respectively). No significant difference between genders was found on RMS and NMF during WT (P > 0.05). Although RPP and RMP were influenced by gender, the RMS and the NMF of the superficial muscles of the QF did not show the same behavior, suggesting that other mechanisms, not related to motor unit recruitment and speed of nervous stimuli in the muscle fiber may be associated to the lower performance of women in high-intensity, short-term exercise.

Inducing mutations in the mouse genome with the chemical mutagen ethylnitrosourea

When compared to other model organisms whose genome is sequenced, the number of mutations identified in the mouse appears extremely reduced and this situation seriously hampers our understanding of mammalian gene function(s). Another important consequence of this shortage is that a majority of human genetic diseases still await an animal model. To improve the situation, two strategies are currently used: the first makes use of embryonic stem cells, in which one can induce knockout mutations almost at will; the second consists of a genome-wide random chemical mutagenesis, followed by screening for mutant phenotypes and subsequent identification of the genetic alteration(s). Several projects are now in progress making use of one or the other of these strategies. Here, we report an original effort where we mutagenized BALB/c males, with the mutagen ethylnitrosourea. Offspring of these males were screened for dominant mutations and a three-generation breeding protocol was set to recover recessive mutations. Eleven mutations were identified (one dominant and ten recessives). Three of these mutations are new alleles (Otop1mlh, Foxn1sepe and probably rodador) at loci where mutations have already been reported, while 4 are new and original alleles (carc, eqlb, frqz, and Sacc). This result indicates that the mouse genome, as expected, is far from being saturated with mutations. More mutations would certainly be discovered using more sophisticated phenotyping protocols. Seven of the 11 new mutant alleles induced in our experiment have been localized on the genetic map as a first step towards positional cloning.

Total hysterectomy versus subtotal hysterectomy: which procedure should be performed during the pregnant-puerperal period?

A retrospective study of 40 hysterectomies due to hemorrhage performed at the "Hospital das Clínicas, Faculdade de Medicina de São Paulo", from January 1978 to August 1989 was conducted in order to determine which type of hysterectomy (total or subtotal) is better indicated during the pregnant-puerperal period. We analyzed operating time, quantity of blood derivatives transfused during the intra- and postoperative periods, time of postoperative hospitalization, number of intra- and postoperative complications, and deaths. The results did not show statistically significant differences between the two types of hysterectomy. We conclude that total hysterectomy is preferable in any clinical situation, especially in the presence of uterine atony and low implanted placenta.

[Acute kidney failure secondary to ophidian bothropic and crotalid accidents. Analysis of 63 cases]

Sessenta e três pacientes com insuficiência renal aguda secundária a acidente ofídico foram tratados no CTI do Hospital das Clínicas da UFMG. Em 32 pacientes (51%) o acidente foi produzido por serpentes do gênero Bothrops (grupo bio-trópico) e em 32 pacientes (49%) pela cascavel sul-americana (grupo crotálico). As principais complicações apresentadas pelos pacientes foram a uremia (100% dos casos), hiperpotassemia (89% dos casos), anemia (78% dos casos), infecção urinária (37% dos casos), hiper-hidratação (17% dos casos), parada cardíaca (14% dos casos) e edema agudo dos pulmões (11% dos casos). Cinco pacientes do grupo crotálico (16%) tiveram insuficiência respiratória aguda atribuída à ação neurotóxica do veneno, quatro dos quais se recuperaram completamente. Sete pacientes do grupo botrópico (22%) tiveram necrose cortical renal diagnosticada em cinco através da biópsia renal e em dois na necropsia. Quarenta e cinco pacientes (71%) foram tratados com diálise peritoneal e a hemodiálise foi necessária em dois pacientes, um dos quais havia sido submetido a diálise peritoneal. Em 17 pacientes (27%) o tratamento foi conservador. Cinqüenta e cinco pacientes receberam alta hospitalar, quatro dos quais com insuficiência renal crônica secundária a necrose cortical renal e oito (13%) faleceram. Os óbitos foram atribuídos a edema pulmonar agudo em quatro pacientes, a estado de choque em dois pacientes e a coma e infecção respiratória após parada cardíaca em dois pacientes.