Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

An update on adenomyosis uteri

Adenomyosis is a gynecological condition commonly encountered in clinical practice. It is defined as the presence of endometrium within the myometrium. The prevalence of this condition in asymptomatic women is unclear, and a large proportion of these women may have associated pathology such as leiomyomas, endometriosis, endometrial polyps, and hyperplasia. Most of the time, diagnosis is made on histological examination of specimen following hysterectomy or adenomyomectomy. We will look at the role of various imaging modalities, such as pelvic ultrasound and magnetic resonance imaging, and their value in improving the accuracy of preoperative diagnosis. Various medical and surgical therapies will also be discussed. Careful counseling on the available treatment options form an important component of clinical care. Hysterectomy is the definitive treatment for women who no longer desire fertility

Single incision laparoscopic surgery in gynecology: Evolution, current trends, and future perspectives

Minimally invasive surgery has become the standard of care for different procedures in various subspecialties. Single-incision laparoscopic surgery (SILS) is a rapidly developing field that may mark the new frontier in laparoscopy. The ongoing and continuous efforts to decrease morbidity and improve cosmesis from laparoscopic surgery has led to minimization in number and size of ports required for these procedures. SILS is laparoscopic surgery performed through a single, small skin incision 15-20 mm in size, usually hidden in the umbilicus. SILS is not a new endeavor, but recent advances in conventional laparoscopic techniques and instrumentation has made SILS more feasible and safer for patients. Within a short span of time there has been an increase in the number of studies and clinical reports depicting the use of SILS in gynecology. As this novel field moves forward, a review of its evolution and current status is requisite. The objective of this article is to review the contemporary literature on SILS in gynecology and the recent advances in techniques and instrumentation used in SILS. The ongoing refinement of surgical techniques and instrumentation has resulted in increasing use of SILS across many subspecialties. Recently published studies have proven the feasibility, safety, and reproducibility of SILS in various gynecologic procedures

Novel Proteomic Biomarker Panel for Prediction of Aggressive Metastatic Hepatocellular Carcinoma Relapse in Surgically Resectable Patients

The natural course of early HCC is unknown, and its progression to intermediate and advanced HCC can be diverse. Some early stage HCC patients enjoy prolonged disease-free survival, whereas others suffer aggressive relapse to stage IV metastatic cancer within a year. Comparative proteomics of HCC tumor tissues was carried out using 2D-DIGE and MALDI-TOF/TOF MS to identify proteins that can distinguish these two groups of stage I HCC patients. Twelve out of 148 differentially regulated protein spots were found to differ by approximately 2-fold for the relapse versus nonrelapse patient tissues. Four proteins, namely, heat shock 70 kDa protein 1, argininosuccinate synthase, isoform 2 of UTP-glucose-1-phosphate uridylyltransferase, and transketolase, were shown to have the potential to differentiate metastatic relapse (MR) from nonrelapse (NR) HCC patients after validation by western blotting and immunohistochemical assays. Subsequent TMA analysis revealed a three marker panel of HSP70, ASS1, and UGP2 to be statistically significant in stratifying the two groups of HCC patients. This combination panel achieved high levels of sensitivity and specificity, which has potential for clinical use in identifying HCC tumors prone to MR. This stratification will allow development of clinical management, including close follow-up and possibly treatment options, in the near future

Novel Proteomic Biomarker Panel for Prediction of Aggressive Metastatic Hepatocellular Carcinoma Relapse in Surgically Resectable Patients

The natural course of early HCC is unknown, and its progression to intermediate and advanced HCC can be diverse. Some early stage HCC patients enjoy prolonged disease-free survival, whereas others suffer aggressive relapse to stage IV metastatic cancer within a year. Comparative proteomics of HCC tumor tissues was carried out using 2D-DIGE and MALDI-TOF/TOF MS to identify proteins that can distinguish these two groups of stage I HCC patients. Twelve out of 148 differentially regulated protein spots were found to differ by approximately 2-fold for the relapse versus nonrelapse patient tissues. Four proteins, namely, heat shock 70 kDa protein 1, argininosuccinate synthase, isoform 2 of UTP-glucose-1-phosphate uridylyltransferase, and transketolase, were shown to have the potential to differentiate metastatic relapse (MR) from nonrelapse (NR) HCC patients after validation by western blotting and immunohistochemical assays. Subsequent TMA analysis revealed a three marker panel of HSP70, ASS1, and UGP2 to be statistically significant in stratifying the two groups of HCC patients. This combination panel achieved high levels of sensitivity and specificity, which has potential for clinical use in identifying HCC tumors prone to MR. This stratification will allow development of clinical management, including close follow-up and possibly treatment options, in the near future

The Future of Adhesion Prophylaxis Trials in Abdominal Surgery: An Expert Global Consensus

Postoperative adhesions represent a frequent complication of abdominal surgery. Adhesions can result from infection, ischemia, and foreign body reaction, but commonly develop after any surgical procedure. The morbidity caused by adhesions affects quality of life and, therefore, it is paramount to continue to raise awareness and scientific recognition of the burden of adhesions in healthcare and clinical research. This 2021 Global Expert Consensus Group worked together to produce consented statements to guide future clinical research trials and advise regulatory authorities. It is critical to harmonize the expectations of research, to both develop and bring to market improved anti-adhesion therapies, with the ultimate, shared goal of improved patient outcomes

A Circulating miRNA Signature for Stratification of Breast Lesions among Women with Abnormal Screening Mammograms

Although mammography is the gold standard for breast cancer screening, the high rates of false-positive mammograms remain a concern. Thus, there is an unmet clinical need for a non-invasive and reliable test to differentiate between malignant and benign breast lesions in order to avoid subjecting patients with abnormal mammograms to unnecessary follow-up diagnostic procedures. Serum samples from 116 malignant breast lesions and 64 benign breast lesions were comprehensively profiled for 2,083 microRNAs (miRNAs) using next-generation sequencing. Of the 180 samples profiled, three outliers were removed based on the principal component analysis (PCA), and the remaining samples were divided into training (n = 125) and test (n = 52) sets at a 70:30 ratio for further analysis. In the training set, significantly differentially expressed miRNAs (adjusted p &lt; 0.01) were identified after correcting for multiple testing using a false discovery rate. Subsequently, a predictive classification model using an eight-miRNA signature and a Bayesian logistic regression algorithm was developed. Based on the receiver operating characteristic (ROC) curve analysis in the test set, the model could achieve an area under the curve (AUC) of 0.9542. Together, this study demonstrates the potential use of circulating miRNAs as an adjunct test to stratify breast lesions in patients with abnormal screening mammograms

Development of a microRNA Panel for Classification of Abnormal Mammograms for Breast Cancer

10.3390/cancers13092130CANCERS13

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe