Clinical implications of tumor-based next-generation sequencing in high-grade epithelial ovarian cancer

BACKGROUND

Tumor-based next-generation sequencing is used inconsistently as a tool to tailor treatment of ovarian cancer, yet beyond detection of somatic BRCA1 and BRCA2 mutations, the clinical benefit is not well established. This study aimed to assess the clinical relevance of tumor-based next-generation sequencing (tbNGS) in patients with ovarian cancer.

METHODS

This retrospective study included patients with high-grade epithelial ovarian carcinoma. tbNGS results were identified in the electronic medical record using optical character recognition and natural language processing. Genetic, clinical, and demographic information was collected. Progression-free survival (PFS) and overall survival were calculated and compared using log-rank tests. Multivariate Cox regression and clustering analyses were used to identify patterns of genetic alterations associated with survival.

RESULTS

Of 1092 patients in the described population, 409 (37.5%) had tbNGS results. Nearly all (96.1% [393/409]) had one or more genetic alterations. In 25.9% (106/409) of patients, an alteration that aligned with a targeted treatment was identified, and in an additional 48.7% (199/409), tbNGS results suggested eligibility for an investigational agent or clinical trial. The most frequent alterations were TP53, PIK3CA, and NF1 mutations, and CCNE1 amplification. Together, BRCA1 and BRCA2 mutations were associated with longer PFS (hazard ratio [HR], 0.62; 95% confidence interval [CI], 0.42-0.92; p = .02), whereas AKT2 amplification was associated with shorter PFS (HR, 3.86; 95% CI, 1.002-14.88; p < .05). Multivariate Cox regression and clustering analyses identified several combinations of genetic alterations that corresponded to outcomes in patients with high-grade serous carcinoma.

CONCLUSIONS

tbNGS often yields clinically relevant information. Detailed analysis of population-level tumor genomics may help to identify therapeutic targets and guide development of clinical decision support tools.

PLAIN LANGUAGE SUMMARY

Although more and more patients with ovarian cancer are undergoing tumor-based next-generation sequencing to identify genetic mutations in their tumors, the benefits of such testing are not well established. In a group of over 400 patients with ovarian cancer who underwent tumor-based next-generation sequencing in the course of their treatment, nearly all patients had one or more genetic alterations detected, and one out of four patients had a mutation that qualified them for a personalized treatment option.

Standardization model for describing the extent of burn injury to human remains

This paper provides a model for standardizing descriptions of the extent of burn injury to human bodies consumed in fire. Its intent is to simplify and make comparable case reports and legal descriptions by medical examiners, pathologists, crime scene investigators, forensic odontologists, forensic anthropologists, fire fighters, paramedics, and others responsible for recovery, analysis, or identification of burn victims. The Crow-Glassman scale (CGS) is divided into five levels depicting increasing destruction to the body relative to burn injury. Each level relates to a unique set of circumstances that may affect on the recovery procedure, analysis strategy for identification, and choice of personnel most suited for making identifications.

Handedness and the bilateral asymmetry of the jugular foramen

This paper examines the proposed association of bilateral asymmetry of the jugular foramen as an indicator of handedness observable from cranial morphology. The jugular foramina of 54 subjects were observed for size asymmetry during routine autopsy procedures. Hand preference data were collected on each subject from family members. Of the 54 subjects, 47 were documented as being right-handed and 7 as being left-handed. These values approximate the average percentage of right-handed versus left-handed individuals from larger populations. Jugular foramen asymmetry was qualitatively identified for 36 subjects (66.7%) and was judged equivocal for the other 18 (33.3%). Of the 36 subjects exhibiting asymmetry, 28 (77.7%) showed positive correlation between the asymmetry direction and handedness. This moderate level of congruence, coupled with the result that 4 of the 7 left-handers exhibited dominant right-side foramina, casts doubt on the reliable use of jugular foramen asymmetry for estimating handedness.

The prevalence of positive test results for Chlamydia trachomatis by direct smear for fluorescent antibodies in a south Texas family planning population

Chlamydia trachomatis is a major human genital pathogen implicated as a leading cause of involuntary infertility in women. To assess the prevalence of results positive for C trachomatis by a direct immunofluorescent test in a family planning population, mass screening of all patients attending five urban family planning clinics was conducted for a two-month period. The objectives of this study were to assess the prevalence of positive C trachomatis test results in this population and to evaluate the commonly accepted demographic/behavioral risk factors reported in previous studies. A total of 2,761 subjects were tested using the MicroTrak collection kit. The subjects ranged in age from 12 to 69 years. The overall rate of positive test results was 10.5%. Significant associations between C trachomatis test results and the following variables were observed: race/ethnicity, age, marital status, existence of multiple partners and positive gonorrhea tests. Chlamydial infection was not significantly associated with income, pregnancy, current contraceptive method or age at first intercourse. While the results of the study indicated both agreement and disagreement with other clinical investigations, the fact that 10.5% of a largely asymptomatic population exhibited chlamydial infection has major implications for the management of women's reproductive health care.

Comparative radiographic study of human and animal long bone patterns

The objective of this study was to test the hypothesis that certain radiographic features can be found to distinguish between human and animal long bone fragments, and therefore would be useful as an adjunct in forensic science identification. Using proposed radiographic criteria, 13 archeologists and 12 dentists were asked to identify 20 radiographic samples as representing human or animal bone. Results showed that archeologists correctly identified 86.8% of the samples, and dentists correctly identified 81.9%. Based on the results of this study, it was concluded that radiographic interpretation of long bone fragments may be a useful aid in a forensic science investigation of human and animal remains.

Principal components analysis of physical growth in savannah baboons

Morphometric data collected from 118 male and 169 female savannah baboons (Papio cynocephalus anubis) aged between birth and 5.5 years were analyzed to describe the morphology and physical growth of this species. Measurements included weight, crown-rump length, triceps circumference, and skinfolds at the neck, subscapular, suprailiac, and triceps anatomical sites. Principal components analyses were applied to the data to provide multivariate assessments of morphological patterning among the variables. These analyses resulted in the extraction of two unrotated orthogonal components that accounted for 88% of the overall sample variation. The first component accounted for 77% of the variation and represents an axis of overall body size. The second component represents an axis of shape variation that contrasts body size with fat patterning, and was interpreted as a measure of body leanness. Individual component scores were computed for determining age, gender, and age-by-gender interaction effects. Both components were found to be age dependent for both genders. Males and females shared similar age patterning along the two components; however, gender differences did occur in patterning along the two components; however, gender differences did occur in respect to leanness. The multivariate measure of overall body size increased for both genders similarly with advancing age. Age patterning along the leanness component was described as a decrease from birth to 1 year, followed by an increase in leanness in older ages. Females had a delayed and significantly less intense increase in leanness relative to males.

Bilateral asymmetry of long arm bones and jugular foramen: implications for handedness

The analysis of asymmetry of the arm long bones and of the cranial jugular foramen has been used to suggest handedness in humans. However, because of the unavailability of documented skeletal material, neither criterion has been systematically tested. If both criteria are associated with handedness, they should also be intercorrelated within individuals. Data were collected from skeletal material of 125 males and 57 females to test whether this intercorrelation exists. According to Chi-square analysis, no statistically significant association was identified. After examining several hypotheses, it was concluded that until further substantiation, neither criterion is related to handedness to a degree appropriate for forensic science identification from skeletal remains.

Technical report: a method for recovering the palmar and plantar pads of small primate cadaver specimens for dermatoglyphic analysis

A method for recovering dermatoglyphic data from tamarin cadavers is described. The method involves the complete removal of the palmar and plantar pads with no destruction to the underlying skeletal elements. Once recovered, the pads are stored in a formalin solution. The stored pads of 213 individuals have remained in a good state of preservation for dermatoglyphic analysis for over four years.

Functional implications of skeletal diversity in two South American tamarins

This study examines the relationship between positional behavior and morphology for two closely related South American tamarin species, Saguinus fuscicollis illigeri and Saguinus oedipus oedipus. Although never systematically documented, the two species are suspected of exhibiting highly similar yet subtly different locomotor behaviors with a greater propensity for climbing, springing, and more powerful leaping in S. oedipus. Fourteen measurements reflecting biomechanical structuring were taken from the postcranial skeleton of 28 individuals of each species. The data were reduced to principal component scores and subjected to a multiple analysis of variance to determine the extent of intergroup skeletal variation. Areas of significant skeletal diversity were interpreted functionally. The results suggest that the differences in functional patterning among the two species is consistent with the behavioral hypothesis. It is concluded that subtle changes in positional behavior may be capable of altering skeletal morphology.