Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer.

PURPOSE: The progression of ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) in humans is highly variable. To better understand the relationship between them, we performed a multi-omic characterization of co-occurring DCIS and IBC lesions in a cohort of individuals. METHODS: Formalin-fixed paraffin-embedded tissue samples from 50 patients with co-occurring DCIS and IBC lesions were subjected to DNA-seq and whole transcriptome RNA-seq. Paired DCIS and IBC multi-omics profiles were then interrogated for DNA mutations, gene expression profiles and pathway analysis. RESULTS: Most small variants and copy number variations were shared between co-occurring DCIS and IBC lesions, with IBC exhibiting on average a higher degree of additional mutations. However, 36% of co-occurring lesions shared no common mutations and 49% shared no common copy number variations. The most frequent genomic variants in both DCIS and IBC were PIK3CA, TP53, KMT2C, MAP3K1, GATA3 and SF3B1, with KMT2C being more frequent in DCIS and TP53 and MAP3K1 more frequent in IBC, though the numbers are too small for definitive conclusions. The most frequent copy number variations were seen in MCL1, CKSB1 and ERBB2. ERBB2 changes were not seen in IBC unless present in the corresponding DCIS. Transcriptional profiles were highly distinct between DCIS and IBC, with DCIS exhibiting upregulation of immune-related signatures, while IBC showed significant overexpression in genes and pathways associated with cell division and proliferation. Interestingly, DCIS and IBC exhibited significant differential expression of different components of extracellular matrix (ECM) formation and regulation, with DCIS showing overexpression of ECM-membrane interaction components while IBC showed upregulation of genes associated with fibronectin and invadopodia. CONCLUSION: While most co-occurring DCIS and IBC were mutationally similar and suggestive of a common clonal progenitor, transcriptionally the lesions are highly distinct, with IBC expressing key pathways that facilitate invasion and proliferation. These results are suggestive of additional levels of regulation, epigenetic or other, that facilitate the acquisition of invasive properties during tumor evolution.

Insights from a Multi-company Workshop to Apply a Patient Participation Burden Algorithm to Protocol Data.

BACKGROUND: Utilizing a participation burden algorithm developed in a previous study, Tufts CSDD, in collaboration with ZS, led a workshop among 8 pharmaceutical companies to validate the methodology of benchmarking the participation burden of a set of retrospective protocols and comparing these data to a prospective protocol design. METHODS: Eight participating companies collected data for 66 retrospective protocols and participation burden scores were calculated for each. Data from one prospective protocol was provided and prospective burden scores were compared to mean retrospective protocol burden for each company. Participating companies provided feedback on data collection process and final reports. RESULTS: Comparisons between retrospective and prospective burden scores revealed higher comparative burden in lab and blood procedures. Companies were able to gather most requested data, but some variables hypothesized to affect burden were not available to sponsors. Time constraints were reported as a challenge throughout the data collection process. CONCLUSIONS: Feedback indicated the need for establishing a larger database to enable comparisons between protocols with the same therapeutic area and indication. Investigating the impact of standard of care burden by indication on overall participation burden and encouraging sponsors to collect more accurate data contributing to participation burden at the site level are also important takeaways from this exercise.

Developmental validation of the ANDE™ rapid DNA system with FlexPlex™ assay for arrestee and reference buccal swab processing and database searching.

A developmental validation was performed to demonstrate reliability, reproducibility and robustness of the ANDE System with the FlexPlex assay, including an integrated Expert System, across a number of laboratories and buccal sample variations. Previously, the related DNAscan™/ANDE 4C Rapid DNA System using the PowerPlex®16 assay and integrated Expert System Software received NDIS approval in March 2016. The enhanced ANDE instrument, referred to as ANDE 6C, and the accompanying 6-dye, 27-locus STR assay, referred to as FlexPlex, have been developed to be compatible with all widely used global loci, including the expanded set of the CODIS core 20 loci. Six forensic and research laboratories participated in the FlexPlex Rapid DNA developmental validation experiments, testing a total of 2045 swabs, including those obtained from 1387 unique individuals. The goal of this extensive and comprehensive validation was to thoroughly evaluate and document the ANDE System and its internal Expert System to reliably genotype reference buccal swab samples in a manner compliant with the FBI's Quality Assurance Standards and the NDIS Operational Procedures. The ANDE System, including automated Expert System analysis, generated reproducible and concordant results for buccal swabs when testing various instruments at different laboratories by a number of different operators. When testing a number of non-human DNAs, including oral bacteria, the ANDE System and FlexPlex assay demonstrated limited cross-reactivity. Potential PCR inhibitors were evaluated as part of the validation and no inhibition was detected. Reproducible and concordant profiles were generated from buccal swab samples collected with a limit of detection appropriate for buccal swab collections from arrestees. The precision and resolution of the System met industry standards for detection of microvariants and single base resolution. The integrated Expert System appropriately demonstrated the ability to correctly pass or fail profiles for CODIS upload without human review. During this comprehensive developmental validation, the ANDE System successfully interpreted over 2000 samples tested with over 99.99% concordant alleles. The data package described herein led to the ANDE System with the FlexPlex assay receiving NDIS approval in June 2018.

Developmental validation of the DNAscan™ Rapid DNA Analysis™ instrument and expert system for reference sample processing.

Since the implementation of forensic DNA typing in labs more than 20 years ago, the analysis procedures and data interpretation have always been conducted in a laboratory by highly trained and qualified scientific personnel. Rapid DNA technology has the potential to expand testing capabilities within forensic laboratories and to allow forensic STR analysis to be performed outside the physical boundaries of the traditional laboratory. The developmental validation of the DNAscan/ANDE Rapid DNA Analysis System was completed using a BioChipSet™ Cassette consumable designed for high DNA content samples, such as single source buccal swabs. A total of eight laboratories participated in the testing which totaled over 2300 swabs, and included nearly 1400 unique individuals. The goal of this extensive study was to obtain, document, analyze, and assess DNAscan and its internal Expert System to reliably genotype reference samples in a manner compliant with the FBI's Quality Assurance Standards (QAS) and the NDIS Operational Procedures. The DNAscan System provided high quality, concordant results for reference buccal swabs, including automated data analysis with an integrated Expert System. Seven external laboratories and NetBio, the developer of the technology, participated in the validation testing demonstrating the reproducibility and reliability of the system and its successful use in a variety of settings by numerous operators. The DNAscan System demonstrated limited cross reactivity with other species, was resilient in the presence of numerous inhibitors, and provided reproducible results for both buccal and purified DNA samples with sensitivity at a level appropriate for buccal swabs. The precision and resolution of the system met industry standards for detection of micro-variants and displayed single base resolution. PCR-based studies provided confidence that the system was robust and that the amplification reaction had been optimized to provide high quality results. The DNAscan integrated Expert System was examined as part of the Developmental Validation and successfully interpreted the over 2000 samples tested with over 99.998% concordant alleles. The system appropriately flagged samples for human review and failed both mixed samples and samples with insufficient genetic information. These results demonstrated the integrated Expert System makes correct allele calls without human intervention.

The critical flux method for reduced filter membrane fouling when monitoring high-solids digesters.

Membrane fouling currently makes filtration of high-solids anaerobic sludges difficult and this is discouraging online monitoring of volatile fatty acids and control of high-solids digesters. The present study tests the critical flux approach to reduce membrane fouling. Filtration tests are performed on two sludges, filtered via a side-stream off two full-scale digesters. Sub-critical flux operating conditions (for minimal cake layer formation) are identified for each of the sludges and the filtration units are operated at these conditions to assess longer term performance. Results for one of the sludges (co-digested primary and secondary sludge) is found to be encouraging, showing that sufficient flux rates (up to 40 L m(-2) h(-1)) can be readily sustained to allow longer term digester monitoring and control. Filtration performance for this sludge did not deteriorate significantly over the test period. Results for the other test sludge (digested thermally hydrolyzed waste activated sludge) were not as favorable and indicated that application may be limited for very high solids digesters (>5% total solids concentration). Differences in filtration behavior for the two test sludges were ascribed to the presence of complex soluble organics, the concentration of sludge solids and their particle size.

A comparative study of root defect coverage using an acellular dermal matrix with and without a recombinant human platelet-derived growth factor.

BACKGROUND: The objective of this case series is to compare root defect coverage results and healing responses of bilateral recession defects treated with acellular dermal matrix (ADM) with and without recombinant human platelet-derived growth factor (rhPDGF). METHODS: Seventeen patients with 40 bilateral gingival recession defects were compared. Each defect was ≥2 mm and treated with ADM and a coronally advanced flap. Using split-mouth design, the control-side ADM was hydrated in sterile saline, whereas the test-side ADM was hydrated in rhPDGF. The patients were evaluated at 1 week, 1 month, 3 months, and 6 months. Standardized measurements were taken preoperatively at 3 and 6 months. Healing was clinically assessed at 1 week and 1 month post-surgically. RESULTS: Both test and control groups showed significant gain in root defect coverage over the 6-month period for all individuals, with the test group showing a 69.0% gain and the control group showing a 76.7% gain. Patients divided into Miller Class I and Class III defects were also found to have a significant gain in root defect coverage over 6 months. The test group showed 84.1% gain, and the control group showed 84.7% gain for Miller Class I defects. For Miller Class III defects, the test group showed 51.5% gain, and the control group showed a 60.8% gain. One week after surgery, 35% of the test group showed better healing, whereas 15% of the control group showed better healing. One month after surgery, 20% of the test group showed better healing, whereas 15% of the control group showed better healing. CONCLUSION: Based on the results of this case series, there were no statistically or clinically significant differences in root defect coverage, keratinized tissue, clinical attachment level, or clinical healing for treatment of root recession with a coronally advanced flap and ADM with and without rhPDGF.