Next generation sequencing in ovarian cancer patients: Does personalized medicine improve oncological outcomes?

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 5553-5553
Author(s):  
Tamar Safra ◽  
Dov Hershkovizh ◽  
Eliya Shachar ◽  
Lyri Adar ◽  
Miriam R. Brezis ◽  
...  

5553 Background: Ovarian cancer (OC) is the second most common gynecologic malignancy and the most common cause of gynecologic cancer mortality in the United States. Homologous recombination deficiency (HRD), including the BRCA mutations, are found in 50% of OC tumors. Next generation sequencing (NGS) provides understanding the underlying molecular and genetic patterns to improve OC treatment. This study examines the prognostic and predictive biomarkers identified with NGS in hopes to improve OC patients outcomes. Methods: The patient cohort included 890 consecutive OC patients treated between 2002 and 2020,at the Tel-Aviv Medical Center. We retrospectively evaluated patients with histopathologically confirmed OC. Cox models were used to analyze the clinical impact of various mutations and biomarkers among OC patients with and without FoundationOne CDx NGS testing, by assessing overall survival (OS), progression free survival (PFS), and physicians' timing preferences for referral to NGS testing. Results: Among the 890 OC patients, 103 (11.57%) completed NGS molecular testing. The median OS among patients with and without NGS testing, adjusted for age, stage and recurrence status, was 73.36 and 68.50 months, respectively (P =.02). The median PFS was 17.23 and 17.43 months, respectively (P =.77). We also evaluated physicians' preferences regarding timing of molecular profiling, upon diagnosis, after first recurrence and at advanced line of treatment in 31.95%, 36.08% and 26.8% of practitioners, respectively. Of the patients who completed NGS, 48 (52.75%) harbored actionable mutations, and 21 patients (43.75%) received matched targeted therapy. Forty-five patients were microsatellite stable (MSS) (45%), 55 with undetermined status (55%) and 0 patients with MSI-H. Forty-one (71.93%) patients had low ( < 5) tumor mutation burden status (TMB), 16 (28.07%) intermediate (5-15) and none with high ( > 15) TMB. There was no noticeable survival difference when comparing low with intermediate TMB (P = 0.3). Loss of heterozygosity (LOH) was a significant prognostic biomarker. Patients with high LOH (hLOH > = 16%) had longer OS compared to low LOH (lLOH < 16%), 99.02 vs. 50.23 months, respectively (P <.005). Patients with hLOH and BRCA mutations (BRCA+) had longer OS compared to hLOH/BRCA WT (BRCA-), lLOH/BRCA+, and lLOH/BRCA-, with an unreached median OS of 91.5 vs. 60.48 vs. 45.21 months, respectively (P =.005). Conclusions: Our work demonstrates the clinical benefit of NGS personalized medicine as a cornerstone of future treatment strategies in OC. Our study suggests an OS benefit among the NGS tested cohort. We identified LOH as a prognostic biomarker. Prospective studies evaluating larger cohorts are necessary to generate a more extensive evaluation of additional prognostic and predictive biomarkers among OC patients.

2019 ◽  
Vol 60 (10) ◽  
pp. 914 ◽  
Author(s):  
Yong Jae Lee ◽  
Dachan Kim ◽  
Hyun-Soo Kim ◽  
Kiyong Na ◽  
Jung-Yun Lee ◽  
...  

2018 ◽  
Vol 62 (4) ◽  
pp. e02474-17 ◽  
Author(s):  
Eldin Talundzic ◽  
Shashidhar Ravishankar ◽  
Julia Kelley ◽  
Dhruviben Patel ◽  
Mateusz Plucinski ◽  
...  

ABSTRACT The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhps IRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.


2015 ◽  
Vol 4 (11) ◽  
pp. e1030561 ◽  
Author(s):  
Miran Jang ◽  
Poh-Yin Yew ◽  
Kosei Hasegawa ◽  
Yuji Ikeda ◽  
Keiichi Fujiwara ◽  
...  

2015 ◽  
Vol 17 (6) ◽  
pp. 705-714 ◽  
Author(s):  
Jennifer A. Hempelmann ◽  
Sheena M. Scroggins ◽  
Colin C. Pritchard ◽  
Stephen J. Salipante

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