Tranexamic Acid to Prevent Obstetrical Hemorrhage after Cesarean Delivery.

BACKGROUND: Prophylactic use of tranexamic acid at the time of cesarean delivery has been shown to decrease the calculated blood loss, but the effect on the need for blood transfusions is unclear. METHODS: We randomly assigned patients undergoing cesarean delivery at 31 U.S. hospitals to receive either tranexamic acid or placebo after umbilical-cord clamping. The primary outcome was a composite of maternal death or blood transfusion by hospital discharge or 7 days post partum, whichever came first. Key secondary outcomes were estimated intraoperative blood loss of more than 1 liter (prespecified as a major secondary outcome), interventions for bleeding and related complications, the preoperative-to-postoperative change in the hemoglobin level, and postpartum infectious complications. Adverse events were assessed. RESULTS: A total of 11,000 participants underwent randomization (5529 to the tranexamic acid group and 5471 to the placebo group); scheduled cesarean delivery accounted for 50.1% and 49.2% of the deliveries in the respective groups. A primary-outcome event occurred in 201 of 5525 participants (3.6%) in the tranexamic acid group and in 233 of 5470 (4.3%) in the placebo group (adjusted relative risk, 0.89; 95.26% confidence interval [CI], 0.74 to 1.07; P = 0.19). Estimated intraoperative blood loss of more than 1 liter occurred in 7.3% of the participants in the tranexamic acid group and in 8.0% of those in the placebo group (relative risk, 0.91; 95% CI, 0.79 to 1.05). Interventions for bleeding complications occurred in 16.1% of the participants in the tranexamic acid group and in 18.0% of those in the placebo group (relative risk, 0.90; 95% CI, 0.82 to 0.97); the change in the hemoglobin level was -1.8 g per deciliter and -1.9 g per deciliter, respectively (mean difference, -0.1 g per deciliter; 95% CI, -0.2 to -0.1); and postpartum infectious complications occurred in 3.2% and 2.5% of the participants, respectively (relative risk, 1.28; 95% CI, 1.02 to 1.61). The frequencies of thromboembolic events and other adverse events were similar in the two groups. CONCLUSIONS: Prophylactic use of tranexamic acid during cesarean delivery did not lead to a significantly lower risk of a composite outcome of maternal death or blood transfusion than placebo. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development; ClinicalTrials.gov number, NCT03364491.).

Antimicrobial Dressing versus Standard Dressing in Obese Women Undergoing Cesarean Delivery: A Randomized Controlled Trial.

OBJECTIVE: This study aimed to evaluate the effect of a novel antimicrobial dressing on patient satisfaction and health-related quality of life (HRQoL) following a cesarean delivery. STUDY DESIGN: This was an open-label, single-center, two-arm randomized controlled trial. This study was done at the tertiary center, maternal unit, Galveston, TX. Pregnant women with body mass indices ≥35 kg/m2 were screened for eligibility. Women were randomized to ReliaTect Post-Op Dressing (RELIATECT) or standard wound dressing (STANDARD). Primary outcome was patient satisfaction and HRQoL using validated questionnaires. Secondary outcomes were provider satisfaction, surgical site infection (SSI) rates, and wound complications. RESULTS: In total, 160 women were randomized. Population characteristics were not significant among groups. RELIATECT dressing group had an overall higher score of satisfaction and HRQoL compared with STANDARD group. Women in the RELIATECT group reported less incision odor and incisional pain. Compared with the STANDARD group, most women in RELIATECT dressing group reported better daily activities, self-esteem, personal hygiene, body image, and sleep. Providers reported that the RELIATECT dressing allowed better assessment of the surgical incision site, allowed patients to shower early, and did observe less wound dressing leakage. No differences were found in other secondary end points. CONCLUSION: Postcesarean RELIATECT dressing for wound care in pregnant women with obesity had better patient and provider satisfaction as well as better HRQoL scores. Further, level 1 evidence is needed to assess its impact on SSI rates and wound complication, as this trial was not powered to accomplish this goal. KEY POINTS: · This study was conducted to evaluate RELIATECT on patient satisfaction and HRQoL following a cesarean.. · Post-cesarean RELIATECT dressing for wound care had better HRQoL and patient and provider satisfaction scores.. · This is the first randomized controlled trial evaluating RELIATECT dressing in obese pregnant women undergoing cesarean section..

The Quantose Insulin Resistance Test for Maternal Insulin Resistance: A Pilot Study.

OBJECTIVE: Insulin resistance (IR) increases during pregnancy which can lead to hyperinsulinemia, gestational diabetes mellitus (GDM), and neonatal hypoglycemia (NH), especially in obese women. Glucose tolerance testing (GTT) is used clinically to evaluate IR in pregnancy. Quantose IR score index is a novel blood screen of IR validated in nonpregnant individuals. The score is generated using an algorithm that combines insulin and three biomarkers of fatty acid pathways (α-hydroxybutyrate, oleic acid, linoleoyl-glycerophospocholine). Our objective was to determine the validity of Quantose IR test (Metabolan Inc. Morrisville, NC) in assessing IR in pregnant obese women, as compared with the homeostatic model assessment of insulin resistance (HOMA-IR), and its ability to predict GDM and NH. STUDY DESIGN: Women between 100/7 and 136/7 weeks of gestation with a pre-pregnancy or early pregnancy body mass index more than 30 kg/m2, and no pregestational diabetes, were included. Fasting blood samples were collected at 100/7 to 136/7 (T1) and 240/7 to 280/7 (T2) weeks. Quantose IR and HOMA-IR were calculated. All women underwent an early (T1; indicated for women with obesity) and a T2 glucose tolerance tests. GDM was diagnosed using the two-step approach, and NH was defined as a neonatal glucose less than 40 mg/dL in the first 24 hours of life. Linear regression and receiver operating characteristic curves were used for analysis. RESULTS: The trial enrolled 100 patients. Ten subjects (10%) were diagnosed with GDM in the second trimester and none in the first trimester. At T1, Quantose IR (R2 = 0.48), but not 1-hour glucose tolerance test (R2 = 0.07), correlated with HOMA-IR. Similar correlations were observed at T2. The 1-hour glucose tolerance test followed by HOMA-IR and Quantose IR (area under the curve [AUC]: 0.82, 0.68, and 0.62, respectively) were predictors of GDM. Quantose IR (AUC: 0.74) and 1-hour glucose tolerance test (AUC: 0.72) at T1 and T2 (AUC: 0.75; AUC: 0.93; respectively) were best predictors of NH. The best cut offs, sensitivities, and specificities for prediction of NH were determined. CONCLUSION: Similar to nonpregnant individuals, Quantose IR appears to be a valid measure of IR in obese pregnant women. First trimester Quantose IR is a predictor of GDM diagnosed in the second trimester and NH. Given that it requires a single blood draw and no glucose challenge, it may be a useful test to evaluate and monitor IR in pregnancy. Our findings may be used as pilot data to explore the potential use of Quantose IR in pregnancy further. KEY POINTS: · Traditional testing methods for insulin resistance in pregnancy are often performed late, are time consuming, and unpleasant to patients.. · The first trimester one-step Quantose IR test reflects insulin resistance in pregnancy and predicts GDM and neonatal hypoglycemia.. · This is the first known prospective clinical study validating Quantose IR score index in an obstetrical population at risk for developing GDM..

Fibroblast growth factor receptor 3 alterations and response to immune checkpoint inhibition in metastatic urothelial cancer: a real world experience.

BACKGROUND: FGFR3-altered urothelial cancer (UC) correlates with a non-T cell-inflamed phenotype and has therefore been postulated to be less responsive to immune checkpoint blockade (ICB). Preclinical work suggests FGFR3 signalling may suppress pathways such as interferon signalling that alter immune microenvironment composition. However, correlative studies examining clinical trials have been conflicting as to whether FGFR altered tumours have equivalent response and survival to ICB in patients with metastatic UC. These findings have yet to be validated in real world data, therefore we evaluated clinical outcomes of patients with FGFR3-altered metastatic UC treated with ICB and investigate the underlying immunogenomic mechanisms of response and resistance. METHODS: 103 patients with metastatic UC treated with ICB at a single academic medical center from 2014 to 2018 were identified. Clinical annotation for demographics and cancer outcomes, as well as somatic DNA and RNA sequencing, were performed. Objective response rate to ICB, progression-free survival, and overall survival was compared between patients with FGFR3-alterations and those without. RNA expression, including molecular subtyping and T cell receptor clonality, was also compared between FGFR3-altered and non-altered patients. RESULTS: Our findings from this dataset confirm that FGFR3-altered (n = 17) and wild type (n = 86) bladder cancers are equally responsive to ICB (12 vs 19%, p = 0.73). Moreover, we demonstrate that despite being less inflamed, FGFR3-altered tumours have equivalent T cell receptor (TCR) diversity and that the balance of a CD8 T cell gene expression signature to immune suppressive features is an important determinant of ICB response. CONCLUSIONS: Our work in a real world dataset validates prior observations from clinical trials but also extends this prior work to demonstrate that FGFR3-altered and wild type tumours have equivalent TCR diversity and that the balance of effector T cell to immune suppression signals are an important determinant of ICB response.

Enhancing Next-Generation Sequencing-Guided Cancer Care Through Cognitive Computing.

BACKGROUND: Using next-generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human "molecular tumor boards" (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB. MATERIALS AND METHODS: One thousand eighteen patient cases that previously underwent targeted exon sequencing at the University of North Carolina (UNC) and subsequent analysis by the UNCseq informatics pipeline and the UNC MTB between November 7, 2011, and May 12, 2015, were analyzed with WfG, a cognitive computing technology for genomic analysis. RESULTS: Using a WfG-curated actionable gene list, we identified additional genomic events of potential significance (not discovered by traditional MTB curation) in 323 (32%) patients. The majority of these additional genomic events were considered actionable based upon their ability to qualify patients for biomarker-selected clinical trials. Indeed, the opening of a relevant clinical trial within 1 month prior to WfG analysis provided the rationale for identification of a new actionable event in nearly a quarter of the 323 patients. This automated analysis took <3 minutes per case. CONCLUSION: These results demonstrate that the interpretation and actionability of somatic NGS results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing could potentially improve patient care by providing a rapid, comprehensive approach for data analysis and consideration of up-to-date availability of clinical trials. IMPLICATIONS FOR PRACTICE: The results of this study demonstrate that the interpretation and actionability of somatic next-generation sequencing results are evolving too rapidly to rely solely on human curation. Molecular tumor boards empowered by cognitive computing can significantly improve patient care by providing a fast, cost-effective, and comprehensive approach for data analysis in the delivery of precision medicine. Patients and physicians who are considering enrollment in clinical trials may benefit from the support of such tools applied to genomic data.

Class III Obese Women's Preferences and Concerns for Cesarean Skin Incision: A Multicenter Survey.

Objective This study aims to assess class III obese women's preferences and concerns regarding cesarean delivery (CD) skin incisions. Study Design Through the National Perinatal Research Consortium (NPRC), women with body mass index ≥ 40 kg/m2 at the time of enrollment completed an anonymous survey in English or Spanish. We evaluated seven domains of preferences and concerns about the cesarean skin incision. Results We surveyed 546 women at five NPRC sites. Median age (interquartile range) was 29 (25, 35) years; 364 (66%) were parous and 161 (30%) had a prior CD. Women self-identified race/ethnicity as White (31%), non-Hispanic Black (31%), Hispanic (31%), other (6%), and not reported (1%). A total of 542 women (99%) rated both delivering the baby in the best possible condition and decreasing incision opening/infection risk as important. Women were less likely to rate other domains as important (all p < 0.001), including: having least pain possible, n = 521 (95%); decreasing the risk of complications in the next pregnancy, n = 490 (90%); decreasing interference with breastfeeding, n = 474 (87%); decreasing operative time, n = 388 (71%); and having the least visible incision, n = 369 (68%). Conclusion Women with class III obesity prioritize immediate maternal and fetal safety regarding CD skin incision over other concerns including cosmetic outcome.

High-fructose diet in pregnancy leads to fetal programming of hypertension, insulin resistance, and obesity in adult offspring.

BACKGROUND: Consumption of fructose-rich diets in the United States is on the rise and thought to be associated with obesity and cardiometabolic diseases. OBJECTIVE: We sought to determine the effects of antenatal exposure to high-fructose diet on offspring's development of metabolic syndrome-like phenotype and other cardiovascular disease risk factors later in life. STUDY DESIGN: Pregnant C57BL/6J dams were randomly allocated to fructose solution (10% wt/vol, n = 10) or water (n = 10) as the only drinking fluid from day 1 of pregnancy until delivery. After weaning, pups were started on regular chow, and evaluated at 1 year of life. We measured percent visceral adipose tissue and liver fat infiltrates using computed tomography, and blood pressure using CODA nonivasive monitor. Intraperitoneal glucose tolerance testing with corresponding insulin concentrations were obtained. Serum concentrations of glucose, insulin, triglycerides, total cholesterol, leptin, and adiponectin were measured in duplicate using standardized assays. Fasting homeostatic model assessment was also calculated to assess insulin resistance. P values <.05 were considered statistically significant. RESULTS: Maternal weight, pup number, and average weight at birth were similar between the 2 groups. Male and female fructose group offspring had higher peak glucose and area under the intraperitoneal glucose tolerance testing curve compared with control, and higher mean arterial pressure compared to control. Female fructose group offspring were heavier and had higher percent visceral adipose tissue, liver fat infiltrates, homeostatic model assessment of insulin resistance scores, insulin area under the intraperitoneal glucose tolerance testing curve, and serum concentrations of leptin, and lower concentrations of adiponectin compared to female control offspring. No significant differences in these parameters were noted in male offspring. Serum concentrations of triglycerides or total cholesterol were not different between the 2 groups for either gender. CONCLUSION: Maternal intake of high fructose leads to fetal programming of adult obesity, hypertension, and metabolic dysfunction, all risk factors for cardiovascular disease. This fetal programming is more pronounced in female offspring. Limiting intake of high fructose-enriched diets in pregnancy may have significant impact on long-term health.

Review of multicenter studies by multiple institutional review boards: characteristics and outcomes for perinatal studies implemented by a multicenter network.

OBJECTIVE: The objective of the study was to describe characteristics and outcomes of a review of multisite perinatal studies by individual institutional review boards (IRBs) and identify barriers and opportunities for streamlined IRB review. STUDY DESIGN: We compared the review of 5 collaborative protocols by individual IRBs at National Perinatal Research Consortium centers from 2007 through 2012. Three randomized trials, 1 observational study, and 1 follow-up study of a trial were selected. IRB logs and communications were reviewed and abstracted by trained team members. RESULTS: Seven or 8 IRBs reviewed each protocol. Monthly IRB meeting frequency varied from 1 to 6. Full board review was required by all IRBs for the primary trials but not by all for the observational protocols. The overall duration from submission to approval (P = .024) and number of stipulations (P = .007) differed across protocols but not across IRBs. However, times from submission-to-IRB review (P = .011) and IRB review-to-initial letter (P < .007) differed across sites. Both overall submission-to-approval and initial review-to-approval times increased with the increasing number of IRB review stipulations (both values P < .001). Significant delays (>60 days) were few and not consistent across IRBs or protocols. Most stipulations were stylistic or editorial modifications rather than regulatory requests. All protocols were approved without changes, and no more than 1 IRB meeting was needed at each site. CONCLUSION: Findings confirm unnecessary duplication and variability and some similarities in IRB review processes and outcomes for multisite perinatal studies. This may help guide initiatives to streamline IRB review and reduce research delays and burdens.

Intravenous Iron Compared With Oral Iron Supplementation for the Treatment of Postpartum Anemia: A Randomized Controlled Trial.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT05047211.

Risk Factors for Perinatal Transmission of Hepatitis C Virus.

OBJECTIVE: To estimate the rate of perinatal transmission of hepatitis C virus (HCV) infection, to identify risk factors for perinatal transmission of HCV infection, and to determine the viremic threshold for perinatal transmission. METHODS: This was a prospective, multicenter, observational study of pregnant individuals at less than 24 weeks of gestation screened for HCV infection from 2012 to 2018 in the Eunice Kennedy Shriver National Institute of Child Health and Human Development Maternal-Fetal Medicine Units Network. Individuals found to be HCV antibody-positive were followed throughout pregnancy. Children were followed for evidence of perinatal transmission at 2-6 months (HCV RNA testing) and at 18-24 months (HCV RNA and antibody testing) of life. The primary outcome was perinatal transmission, defined as positive test results at either follow-up time point. RESULTS: A total of 109,379 individuals were screened for HCV infection. Of the 1,224 participants who screened positive, 772 (63.1%) enrolled and 432 of those 772 (56.0%) had data available to assess primary outcome. The overall rate of perinatal transmission was 6.0% (26/432, 95% CI 4.0-8.7%). All children with HCV infection were born to individuals with demonstrable viremia. In viremic participants (n=314), the perinatal transmission rate was 8.0% (95% CI 5.2-11.5%). Risk factors for perinatal transmission included HCV RNA greater than 106 international units/mL (adjusted odds ratio [aOR] 8.22, 95% CI 3.16-21.4) and vaginal bleeding reported at any time before delivery (aOR 3.26, 95% CI 1.32-8.03). A viremic threshold for perinatal transmission could not be established. CONCLUSION: Perinatal transmission of HCV infection was limited to viremic individuals. High viral loads and antepartum bleeding were associated with perinatal transmission.

Tumor Cell Extrinsic Synaptogyrin 3 Expression as a Diagnostic and Prognostic Biomarker in Head and Neck Cancer.

Over 70% of oropharyngeal head and neck squamous cell carcinoma (HNSC) cases in the United States are positive for human papillomavirus (HPV) yet biomarkers for stratifying oropharyngeal head and neck squamous cell carcinoma (HNSC) patient risk are limited. We used immunogenomics to identify differentially expressed genes in immune cells of HPV(+) and HPV(-) squamous carcinomas. Candidate genes were tested in clinical specimens using both quantitative RT-PCR and IHC and validated by IHC using the Carolina Head and Neck Cancer Study (CHANCE) tissue microarray of HNSC cases. We performed multiplex immunofluorescent staining to confirm expression within the immune cells of HPV(+) tumors, receiver operating characteristic (ROC) curve analyses, and assessed survival outcomes. The neuronal gene Synaptogyrin-3 (SYNGR3) is robustly expressed in immune cells of HPV(+) squamous cancers. Multiplex immunostaining and single cell RNA-seq analyses confirmed SYNGR3 expression in T cells, but also unexpectedly in B cells of HPV(+) tumors. ROC curve analyses revealed that combining SYNGR3 and p16 provides more sensitivity and specificity for HPV detection compared to p16 IHC alone. SYNGR3-high HNSC patients have significantly better prognosis with five-year OS and DSS rates of 60% and 71%, respectively. Moreover, combining p16 localization and SYNGR3 expression can further risk stratify HPV(+) patients such that high cytoplasmic, low nuclear p16 do significantly worse (Hazard Ratio, 8.6; P = 0.032) compared to patients with high cytoplasmic, high nuclear p16. SYNGR3 expression in T and B cells is associated with HPV status and enhanced survival outcomes of HNSC patients.

UNMASC: tumor-only variant calling with unmatched normal controls.

Despite years of progress, mutation detection in cancer samples continues to require significant manual review as a final step. Expert review is particularly challenging in cases where tumors are sequenced without matched normal control DNA. Attempts have been made to call somatic point mutations without a matched normal sample by removing well-known germline variants, utilizing unmatched normal controls, and constructing decision rules to classify sequencing errors and private germline variants. With budgetary constraints related to computational and sequencing costs, finding the appropriate number of controls is a crucial step to identifying somatic variants. Our approach utilizes public databases for canonical somatic variants as well as germline variants and leverages information gathered about nearby positions in the normal controls. Drawing from our cohort of targeted capture panel sequencing of tumor and normal samples with varying tumortypes and demographics, these served as a benchmark for our tumor-only variant calling pipeline to observe the relationship between our ability to correctly classify variants against a number of unmatched normals. With our benchmarked samples, approximately ten normal controls were needed to maintain 94% sensitivity, 99% specificity and 76% positive predictive value, far outperforming comparable methods. Our approach, called UNMASC, also serves as a supplement to traditional tumor with matched normal variant calling workflows and can potentially extend to other concerns arising from analyzing next generation sequencing data.

Characteristics Associated With Consent and Reasons for Declining in a Randomized Trial in Pregnancy.

OBJECTIVE: To evaluate the maternal characteristics associated with consent to a randomized trial of labor induction in pregnancy. METHODS: This is a secondary analysis of low-risk nulliparous women randomized to induction of labor at 39 weeks or expectant management. During the trial, the Data and Safety Monitoring Committee requested additional fields on the screening log, which already included race and ethnicity: maternal age, type of insurance, and the reason for declining consent if declined. RESULTS: From August 2016 (start of additional data collection) to August 2017, 1,965 (28%) of the 7,112 eligible women consented to the trial. Consent was more likely for Black women (41%, adjusted odds ratio [aOR] 1.47, 95% CI 1.24-1.74), and less likely for Asian women (15%, aOR 0.64, 95% CI 0.48-0.84), compared with White women (24%). Women without private insurance were more likely to consent (38%, aOR 1.55, 95% CI 1.34-1.79), compared with those with private insurance (22%). Younger women were also more likely to consent. Among eligible women who declined participation and provided a reason (68%), preference to be expectantly managed (85%) was most common, a response more common in Asian women (aOR 1.75, 95% CI 1.31-2.33) and less common in women without private insurance (aOR 0.60, 95% CI 0.51-0.70). Not wanting to participate in research was more common in Asian women (aOR 2.41, 95% CI 1.44-4.03). Declining consent because family or friends objected was more common in Asian women (aOR 2.51, 95% CI 1.27-4.95) and women without private insurance (aOR 1.68, 95% CI 1.10-2.59). CONCLUSION: Frequency of consent and reasons for declining consent were associated with age, type of insurance, and race and ethnicity. These findings should be considered when developing recruitment strategies that promote diverse participant representation. CLINICAL TRIAL REGISTRATION: ClinialTrials.gov, NCT01990612.

Hepatitis C Virus Antibody Screening in a Cohort of Pregnant Women: Identifying Seroprevalence and Risk Factors.

OBJECTIVE: To describe the prevalence of hepatitis C virus (HCV) antibody, evaluate current risk factors associated with HCV antibody positivity, and identify novel composite risk factors for identification of groups most likely to demonstrate HCV antibody seropositivity in an obstetric population from 2012 to 2015. METHODS: The Eunice Kennedy Shriver National Institute of Child Health and Human Development Maternal-Fetal Medicine Units Network initiated an observational study of mother-to-child transmission of HCV in 2012 that included offering HCV antibody screening to their entire obstetric population. Women presenting for prenatal care before 23 weeks of gestation without a known multifetal gestation were eligible. For each woman who was HCV antibody-positive, two women at similar gestational age who were HCV antibody-negative were identified and included for comparison. Risk factors were evaluated by patient interview and chart review. Women in the case group were identified to have a signal-to-cutoff value of at least 5 on the Abbott ARCHITECT platform. RNA status was evaluated for women in the case group. RESULTS: Of 106,842 women screened for the HCV antibody, 254 had positive results. The HCV antibody seroprevalence rate was 2.4 cases per 1,000 women (95% CI 2.1-2.7). One hundred thirty-one women in the case group and 251 women in the control group were included in the case-control analysis. Factors associated with HCV antibody positivity included injection drug use (adjusted odds ratio [aOR] 22.9, 95% CI 8.2-64.0), blood transfusion (aOR 3.7, 95% CI 1.3-10.4), having a partner with HCV (aOR 6.3, 95% CI 1.8-22.6), more than three lifetime sexual partners (aOR 5.3, 95% CI 1.4-19.8), and smoking (aOR 2.4, 95% CI 1.2-4.6). A composite of any of these potential risk factors provided the highest sensitivity for detecting HCV antibody (75/82 cases, 91%). CONCLUSION: In this cohort, the seroprevalence of HCV antibody was low, and the current risk factors for HCV screening were not identified. These findings may be useful in defining new strategies for identifying mothers with the HCV antibody and the neonates susceptible to maternal transmission of HCV. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT01959321.

Correction: Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes.

[This corrects the article DOI: 10.1371/journal.pone.0056823.].

The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma.

Background: Little is known about the prognostic significance of somatically mutated genes in metastatic melanoma (MM). We have employed a combined clinical and bioinformatics approach on tumor samples from cutaneous melanoma (SKCM) as part of The Cancer Genome Atlas project (TCGA) to identify mutated genes with potential clinical relevance. Methods: After limiting our DNA sequencing analysis to MM samples (n = 356) and to the CANCER CENSUS gene list, we filtered out mutations with low functional significance (snpEFF). We performed Cox analysis on 53 genes that were mutated in ≥3% of samples, and had ≥50% difference in incidence of mutations in deceased subjects versus alive subjects. Results: Four genes were potentially prognostic [RAC1, FGFR1, CARD11, CIITA; false discovery rate (FDR) < 0.2]. We identified 18 additional genes (e.g., SPEN, PDGFRB, GNAS, MAP2K1, EGFR, TSC2) that were less likely to have prognostic value (FDR < 0.4). Most somatic mutations in these 22 genes were infrequent (< 10%), associated with high somatic mutation burden, and were evenly distributed across all exons, except for RAC1 and MAP2K1. Mutations in only 9 of these 22 genes were also identified by RNA sequencing in >75% of the samples that exhibited corresponding DNA mutations. The low frequency, UV signature type and RNA expression of the 22 genes in MM samples were confirmed in a separate multi-institution validation cohort (n = 413). An underpowered analysis within a subset of this validation cohort with available patient follow-up (n = 224) showed that somatic mutations in SPEN and RAC1 reached borderline prognostic significance [log-rank favorable (p = 0.09) and adverse (p = 0.07), respectively]. Somatic mutations in SPEN, and to a lesser extent RAC1, were not associated with definite gene copy number or RNA expression alterations. High (>2+) nuclear plus cytoplasmic expression intensity for SPEN was associated with longer melanoma-specific overall survival (OS) compared to lower (≤ 2+) nuclear intensity (p = 0.048). We conclude that expressed somatic mutations in infrequently mutated genes beyond the well-characterized ones (e.g., BRAF, RAS, CDKN2A, PTEN, TP53), such as RAC1 and SPEN, may have prognostic significance in MM.

What we have learned about best practices for recruitment and retention in multicenter pregnancy studies.

For 30 years, the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Units (MFMU) Network has had significant impact on clinical practice in obstetrics. The MFMU Network has conducted 50 randomized clinical trials and observational studies designed to improve pregnancy outcomes for mothers and children. Each center has a designated clinical research nurse coordinator who coordinates the day-to-day operations of each trial and leads a research team that is responsible for recruitment and retention of participants. Some of the lessons learned by the nurse coordinators over the past 30 years are described with examples from recent studies. Best practices that we have amassed from our experience are also described.

Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.

The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS) panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV) as well as small insertions and deletions (indel). In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV), similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07-0120 tissue cohort) and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11-1115 tissue cohort) and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion.

Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.

Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous disease. Beyond the role of human papilloma virus (HPV), no validated molecular characterization of the disease has been established. Using an integrated genomic analysis and validation methodology we confirm four molecular classes of HNSCC (basal, mesenchymal, atypical, and classical) consistent with signatures established for squamous carcinoma of the lung, including deregulation of the KEAP1/NFE2L2 oxidative stress pathway, differential utilization of the lineage markers SOX2 and TP63, and preference for the oncogenes PIK3CA and EGFR. For potential clinical use the signatures are complimentary to classification by HPV infection status as well as the putative high risk marker CCND1 copy number gain. A molecular etiology for the subtypes is suggested by statistically significant chromosomal gains and losses and differential cell of origin expression patterns. Model systems representative of each of the four subtypes are also presented.