Evaluation of the 3dMDface system as a tool for soft tissue analysis

OBJECTIVES

To evaluate the accuracy of three-dimensional stereophotogrammetry by comparing values obtained from direct anthropometry and the 3dMDface system. To achieve a more comprehensive evaluation of the reliability of 3dMD, both linear and surface measurements were examined.

SETTING AND SAMPLE POPULATION

UCLA Section of Orthodontics. Mannequin head as model for anthropometric measurements.

MATERIAL AND METHODS

Image acquisition and analysis were carried out on a mannequin head using 16 anthropometric landmarks and 21 measured parameters for linear and surface distances. 3D images using 3dMDface system were made at 0, 1 and 24 hours; 1, 2, 3 and 4 weeks. Error magnitude statistics used include mean absolute difference, standard deviation of error, relative error magnitude and root mean square error. Intra-observer agreement for all measurements was attained.

RESULTS

Overall mean errors were lower than 1.00 mm for both linear and surface parameter measurements, except in 5 of the 21 measurements. The three longest parameter distances showed increased variation compared to shorter distances. No systematic errors were observed for all performed paired t tests (P<.05). Agreement values between two observers ranged from 0.91 to 0.99.

CONCLUSIONS

Measurements on a mannequin confirmed the accuracy of all landmarks and parameters analysed in this study using the 3dMDface system. Results indicated that 3dMDface system is an accurate tool for linear and surface measurements, with potentially broad-reaching applications in orthodontics, surgical treatment planning and treatment evaluation.

European Association for the Study of the Liver (EASL), European Association for the Study of Diabetes (EASD) and European Association for the Study of Obesity (EASO) clinical practice recommendations for the management of non-alcoholic fatty liver disease: evaluation of their application in people with Type 2 diabetes

AIMS

To evaluate the application of the recently proposed recommendations by the European Association for the Study of the Liver, European Association for the Study of Diabetes and European Association for the Study of Obesity for the diagnosis, treatment and follow-up of non-alcoholic fatty liver disease in people with Type 2 diabetes.

METHODS

A total of 179 people with Type 2 diabetes were included in this study. Liver fat content (assessed using proton magnetic resonance spectroscopy), fatty liver index score, non-alcoholic fatty liver disease fibrosis score, and SteatoTest and FibroTest scores were determined.

RESULTS

According to proton magnetic resonance spectroscopy, 68.7% of participants had steatosis (liver fat content >5.5%). The application of the guidelines using several combinations (fatty liver index + non-alcoholic fatty liver disease fibrosis scores, Steatotest + FibroTest scores, proton magnetic resonance spectroscopy + non-alcoholic fatty liver disease fibrosis score, proton magnetic resonance spectroscopy + FibroTest) resulted in a referral to a liver clinic for 33.5-84.9% people with Type 2 diabetes.

CONCLUSIONS

The application of these new algorithms for the diagnosis, and follow-up of non-alcoholic fatty liver disease would lead to an excessive number of people with Type 2 diabetes being referred to a liver clinic. We suggest that new clinical and/or biological biomarkers of steatosis and fibrosis be specifically validated in people with Type 2 diabetes.

Abstract P1-07-20: Developing prognostic indicators of poor outcomes in PRAEGNANT metastatic breast cancer cohort

Background: Despite novel, targeted therapies, metastatic breast cancer patients have an extremely unfavourable prognosis. Prognostic and predictive factors for patients with advanced breast cancer are not well understood. Molecular assessment of the patient and the tumor in the metastatic situation is not routinely performed despite advances in molecular precision medicine indicating great benefit to this patient group. Here we present early findings from the first 142 patients of a prospective molecular breast cancer registry with completed transcriptomic profiling.

Methods: The PRAEGNANT study proctocol (NCT02338767) is a molecular registry designed to provide an infrastructure for the real-time comprehensive analysis of tumor and patient molecular characteristics under study conditions. Formalin fixed paraffin embedded tumors have been used from this registry to identify molecular, transcriptomic predictors for overall survival (OS).

Known clinical correlates for OS (e.g. hormone-receptor status, age at diagnosis, and BMI) were analyzed by Cox proportional hazard ratios, and compared to transcriptomic markers of outcomes. Transcriptomes for all patient tumors were sequenced on the Illumina sequencing platform, and analyzed by RSEM to estimate transcripts per million (TPM) values for each gene isoform. Log-TPM values were used in established (PAM50) and novel (hierarchical clustering) expression-based subtyping of tumor samples. Expression-based subtypes were demonstrated to be strong prognostic indicators by Cox analysis. A Lasso regression machine learning algorithm was used to develop an expression-based predictive model of OS.

Results: Hormone receptor positivity (HR=0.7, p&lt;0.006) and TNBC status (HR=1.4, p&lt;0.01) were significantly associated with outcomes. PAM50 subtypes were also strong indicators of outcomes (e.g. Basal disease compared to Luminal-A subtype has HR=1.4, p&lt;0.017). A novel expression-based high-risk cluster in this cohort was more indicative of poor prognosis than clinical variates or Basal-type, with a HR=2.7 (p&lt;0.009) when compared to Luminal-A subtype. An expression-based survival prediction model achieved a concordance-index of 0.65 in an unseen validation cohort. Patients predicted as having the shortest survival times were in the high-risk cluster.

Conclusions: Here we demonstrate using molecular profiling to develop prognostic signatures that out-perform standard clinical correlates of poor outcomes, even in a small subset of the total cohort. As the PRAEGNANT cohort expands these prognostic tools will continue to improve and supplement physician knowledge to improve patient outcomes.

Citation Format: Szeto C, Benz S, Nguyen A, Rübner M, Wallwiener D, Tesch H, Hadji P, Fehm TN, Janni W, Overkamp F, Lueftner D, Lux MP, Wallwiener M, Beckmann MW, Huebner H, Ettl J, Hartkopf AD, Mueller V, Taran FA, Belleville E, Schneeweiss A, Soon-Shiong P, Rabizadeh S, Fasching PA. Developing prognostic indicators of poor outcomes in PRAEGNANT metastatic breast cancer cohort [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-07-20.

Quantification of M13 and T7 bacteriophages by TaqMan and SYBR green qPCR

TaqMan and SYBR Green quantitative PCR (qPCR) methods were developed as DNA-based approaches to reproducibly enumerate M13 and T7 phages from phage display selection experiments individually and simultaneously. The genome copies of M13 and T7 phages were quantified by TaqMan or SYBR Green qPCR referenced against M13 and T7 DNA standard curves of known concentrations. TaqMan qPCR was capable of quantifying M13 and T7 phage DNA simultaneously with a detection range of 2.75*10¹-2.75*10⁸genome copies(gc)/μL and 2.66*10¹-2.66*10⁸ genome copies(gc)/μL respectively. TaqMan qPCR demonstrated an efficient amplification efficiency (E_s) of 0.97 and 0.90 for M13 and T7 phage DNA, respectively. SYBR Green qPCR was ten-fold more sensitive than TaqMan qPCR, able to quantify 2.75-2.75*10⁷gc/μL and 2.66*10¹-2.66*10⁷gc/μL of M13 and T7 phage DNA, with an amplification efficiency E_s of 1.06 and 0.78, respectively. Due to its superior sensitivity, SYBR Green qPCR was used to enumerate M13 and T7 phage display clones selected against a cell line, and quantified titers demonstrated accuracy comparable to titers from traditional double-layer plaque assay. Compared to enzyme linked immunosorbent assay, both qPCR methods exhibited increased detection sensitivity and reproducibility. These qPCR methods are reproducible, sensitive, and time-saving to determine their titers and to quantify a large number of phage samples individually or simultaneously, thus avoiding the need for time-intensive double-layer plaque assay. These findings highlight the attractiveness of qPCR for phage enumeration for applications ranging from selection to next-generation sequencing (NGS).

Survival after treatment with curative intent for hepatocellular carcinoma among patients with vs without non-alcoholic fatty liver disease

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is expected to become a leading aetiology of hepatocellular carcinoma (HCC)-related mortality in the United States. HCC treatments with curative intent (OLT, orthotopic liver transplantation; resection; RFA, radiofrequency ablation) can improve survival in carefully selected patients.

AIM

To compare survival after receipt of curative treatment for NAFLD and non-NAFLD-HCC aetiologies (HCV, chronic hepatitis C; HBV, chronic hepatitis B; ALD, alcoholic liver disease) and by treatment was performed.

METHODS

A cohort of 17 664 patients was assembled using linked Surveillance, Epidemiology, and End Results and Medicare data from 1991 to 2011 with confirmed diagnosis of HCC.

RESULTS

The cohort was mostly male, aged 70 (21-106) years, without cardiovascular disease, and had liver cirrhosis without decompensation, metastatic HCC or large tumour size (>5 cm). The NAFLD-HCC group was mostly female and older with more cardiovascular disease, metastatic HCC, and large tumour size and less cirrhosis and decompensated liver disease than the non-NAFLD-HCC groups. The NAFLD group was 47% less likely to receive any curative treatment as compared with non-NAFLD aetiologies (OR 0.53, P < .001). NAFLD-HCC had worse median survival after OLT (3.2, 0-12.9 years, P = .01) but had improved survival after resection (2.4, 0-12.0 years, P < .001) as compared with non-NAFLD-HCC. No significant survival differences existed for RFA by HCC aetiology. NAFLD was not an independent predictor of mortality after OLT, resection or RFA.

CONCLUSION

Patients with NAFLD-HCC had worse survival after OLT but favourable survival after resection, particularly in the absence of cirrhosis, as compared with non-NAFLD-HCC aetiologies.