Long term toxicity of intracranial germ cell tumor treatment in adolescents and young adults.

PURPOSE: The purpose of this study is to describe the long-term toxicities of intracranial germ cell tumor (IGCT) in the adolescent and young adult (AYA) population. METHODS: We report late toxicities of a multi-center cohort of AYA patients treated for IGCT between 1975 and 2015. Charts were retrospectively reviewed for hormone deficiency, ototoxicity, seizure disorder, visual deterioration, cerebrovascular events, second neoplasm, psychiatric illness, and neurocognitive impairment. Statistical analysis was performed for late toxicities to evaluate the influence of select factors. RESULTS: Our patient cohort included 112 patients with IGCTs; 84% of patients had a germinoma as opposed to a non-germinomatous germ cell tumor (NGGCT), median age at radiotherapy (RT) was 19 years, and median follow-up was 8.3 years. Of the 94 patients with germinoma, 32 (34%) received both chemotherapy and RT as part of their upfront treatment, while 62 (66%) received RT alone. All 18 patients with NGGCT received chemotherapy and RT. The most common late toxicity following IGCT treatments was physician-reported neurocognitive impairment, with a 10-year cumulative incidence (CI) of 38.5%. Ten-year CI of treatment-induced ototoxicity was 39.2% for patients who received cisplatin, compared to 3.6% for those who received carboplatin but no cisplatin (p < 0.005). Suprasellar/hypothalamic tumor location was associated with 10-year CI of treatment-induced hormone deficiency (36.1 vs 6.2%, p < 0.005). CONCLUSIONS: A significant proportion of AYAs treated for IGCTs experience late effects from treatment, including neurocognitive impairment, ototoxicity, and hormone deficiency. Suprasellar/hypothalamic tumor location and cisplatin were associated with a higher risk of treatment-induced hormone deficiency and ototoxicity, respectively.

A randomized double-blind trial to measure the absorption characteristics of eicosapentaenoic acid and docosahexaenoic acid rich oil blend with natural lipid-based delivery system.

A randomized, double-blinded trial with 65 subjects was conducted to compare the pharmacokinetics between PhytoMarineCelle (PM) that consists of eicosapentaenoic acid and docosahexaenoic acid (EPA + DHA) plus a self-emulsifying drug delivery system (SEDDS), and a standard EPA + DHA ethyl ester (SEE) that does not contain SEDDS. PM showed 1.6-fold greater plasma area under the curve (AUC) than SEE at 300 mg, although no significant difference was observed. PM showed a 3.1 and 3.2-fold (p < 0.05) greater plasma AUC than SEE at 500 mg and 1000 mg respectively. The concentration max (Cmax) of EPA + DHA did not change between PM and SEE at 300 mg. Cmax of PM was twofold greater than SEE at 500 mg and 1000 mg respectively. The Cmax of EPA + DHA achieved significant difference (p < 0.05) only with the 500 mg dose. The PM formulation increased the bioavailability of EPA + DHA by threefold compared to SEE at 500 and 1000 mg.

Repeatability and reproducibility of prostate apparent diffusion coefficient values on a 1.5 T magnetic resonance linear accelerator.

Background and Purpose: Integrated magnetic resonance linear accelerator (MR-Linac) systems offer potential for biologically based adaptive radiation therapy using apparent diffusion coefficient (ADC). Accurate tracking of longitudinal ADC changes is key to establishing ADC-driven dose adaptation. Here, we report repeatability and reproducibility of intraprostatic ADC using deformable image registration (DIR) to correct for inter-fraction prostate changes. Materials and Methods: The study included within-fraction repeat ADC measurements for three consecutive fractions for 20 patients with prostate cancer treated on a 1.5 T MR-Linac. We deformably registered successive fraction T2-weighted images and applied the deformation vector field to corresponding ADC maps to align to fraction 2. We delineated gross tumour volume (GTV), peripheral zone (PZ) and prostate clinical target volume (CTV) regions-of-interest (ROIs) on T2-weighted MRI and copied to ADC maps. We computed intraclass correlation coefficients (ICC) and percent repeatability coefficient (%RC) to determine within-fraction repeatability and between-fraction reproducibility for individual voxels, mean and 10th percentile ADC values per ROI. Results: The ICC between repeats and fractions was excellent for mean and 10th percentile ADC in all ROIs (ICC > 0.86), and moderate repeatability and reproducibility existed for individual voxels (ICC > 0.542). Similarly, low %RC within-fraction (4.2-17.9 %) mean and 10th percentile ADC existed, with greater %RC between fractions (10.2-36.8 %). Higher %RC existed for individual voxel within-fraction (21.7-30.6 %) and between-fraction (32.1-34.5 %) ADC. Conclusions: Results suggest excellent ADC repeatability and reproducibility in clinically relevant ROIs using DIR to correct between-fraction anatomical changes. We established the precision of voxel-level ADC tracking for future biologically based adaptation implementation.

Prospective evaluation of patient-reported anxiety and experiences with adaptive radiation therapy on an MR-linac.

Purpose: An integrated magnetic resonance scanner and linear accelerator (MR-linac) was implemented with daily online adaptive radiation therapy (ART). This study evaluated patient-reported experiences with their overall hospital care as well as treatment in the MR-linac environment. Methods: Patients pre-screened for MR eligibility and claustrophobia were referred to simulation on a 1.5 T MR-linac. Patient-reported experience measures were captured using two validated surveys. The 15-item MR-anxiety questionnaire (MR-AQ) was administered immediately after the first treatment to rate MR-related anxiety and relaxation. The 40-item satisfaction with cancer care questionnaire rating doctors, radiation therapists, the services and care organization and their outpatient experience was administered immediately after the last treatment using five-point Likert responses. Results were analyzed using descriptive statistics. Results: 205 patients were included in this analysis. Multiple sites were treated across the pelvis and abdomen with a median treatment time per fraction of 46 and 66 min respectively. Patients rated MR-related anxiety as "not at all" (87%), "somewhat" (11%), "moderately" (1%) and "very much so" (1%). Positive satisfaction responses ranged from 78 to 100% (median 93%) across all items. All radiation therapist-specific items were rated positively as 96-100%. The five lowest rated items (range 78-85%) were related to general provision of information, coordination, and communication. Overall hospital care was rated positively at 99%. Conclusion: In this large, single-institution prospective cohort, all patients had low MR-related anxiety and completed treatment as planned despite lengthy ART treatments with the MR-linac. Patients overall were highly satisfied with their cancer care involving ART using an MR-linac.

Comparison of ventilation and voice outcomes between unilateral laryngeal pacing and unilateral cordotomy for the treatment of bilateral vocal fold paralysis.

BACKGROUND/AIMS: Rehabilitation of the bilaterally paralyzed human larynx remains a complex clinical problem. Conventional treatment generally involves surgical enlargement of the compromised airway, but often with resultant dysphonia and risk of aspiration. In this retrospective study, we compared one such treatment, posterior cordotomy, with unilateral laryngeal pacing: reanimation of vocal fold opening by functional electrical stimulation of the posterior cricoarytenoid muscle. METHODS: Postoperative peak inspiratory flow (PIF) values and overall voice grade ratings were compared between the two surgical groups, and pre- and postoperative PIF were compared within the pacing group. RESULTS: There were 5 patients in the unilateral pacing group and 12 patients in the unilateral cordotomy group. Within the pacing group, postoperative PIF values were significantly improved from preoperative PIF values (p = 0.04) without a significant effect on voice (grade; p = 0.62). Within the pacing group, the mean postoperative PIF value was significantly higher than that in the cordotomy group (p = 0.05). Also, the mean postoperative overall voice grade values in the pacing group were significantly lower (better) than those of the cordotomy group (p = 0.03). CONCLUSION: Unilateral pacing appears to be an effective treatment superior to posterior cordotomy with respect to postoperative ventilation and voice outcome measures.

The dosimetric underpinning of bladder filling criteria for prostate image-guided volumetric modulated arc therapy.

OBJECTIVES: Repeated CT simulation imaging is common at our institution due to failure to achieve acceptable bladder filling in patients undergoing prostate radiotherapy. There is operational value in re-assessing the validity of the bladder filling assessment criteria by comparing the quality of two plans optimized based on either an "Accepted" or "Rejected" bladder status. METHODS: Twenty prostate patients with repeated CT simulation imaging were included. For each patient, a VMAT plan created using the "Rejected" bladder was compared with the "Accepted" bladder plan. Then, delivered dose to bladder was estimated using ≥4 CBCTs to measure number of fractions with major bladderdose violation (>5% difference) for both plans. Bladder heights of fractions without major bladder dose violations were compared to those with a violation to determine a threshold height for bladder filling acceptability. RESULTS: Using the "Accepted" bladder plans for treatment resulted in 30/175 fractions with major dose violations. These 30 bladders were significantly shorter than those without major violation (mean 28 vs 43mm, p < 0.05). The "Rejected" bladder plans delivered a lower dose to the bladder by ≥5% than the '"Accepted" bladder plans in 59% of fractions, and the number of fractions with major dose violations was 17. CONCLUSIONS: Using a shorter bladder for plan optimization resulted in better bladder sparing during treatment and improved compliance to protocol specific bladder dose constraints. A bladder height range of 20-40 mm measured between the bladder dome and the superior aspect of the symphysis pubis is recommended for prostate radiotherapy requiring a full bladder protocol. ADVANCES IN KNOWLEDGE: Using real patient data from simulation and treatment, this study established a range of bladder height that can be measured easily in a clinical setting for assessing adequacy of bladder filling for prostate radiotherapy.

Practice-based training strategy for therapist-driven prostate MR-Linac adaptive radiotherapy.

Purpose: To develop a practice-based training strategy to transition from radiation oncologist to therapist-driven prostate MR-Linac adaptive radiotherapy. Methods and materials: In phase 1, 7 therapists independently contoured the prostate and organs-at-risk on T2-weighted MR images from 11 previously treated MR-Linac prostate patients. Contours were evaluated quantitatively (i.e. Dice similarity coefficient [DSC] calculated against oncologist generated online contours) and qualitatively (i.e. oncologist using a 5-point Likert scale; a score ≥ 4 was deemed a pass, a 90% pass rate was required to proceed to the next phase). Phase 2 consisted of supervised online workflow with therapists required no intervention from the oncologist on 10 total cases to advance. Phase 3 involved unsupervised therapist-driven workflow, with offline support from oncologists prior to the next fraction. Results: In phase 1, the mean DSC was 0.92 (range 0.85-0.97), and mean Likert score was 3.7 for the prostate. Five therapists did not attain a pass rate (3-5 cases with prostate contour score < 4), underwent follow-up one-on-one review, and performed contours on a further training set (n = 5). Each participant completed a median of 12 (range 10-13) cases in phase 2; of 82 cases, minor direction were required from the oncologist on 5 regarding target contouring. Radiation oncologists reviewed 179 treatment fractions in phase 3, and deemed 5 cases acceptable but with suggestions for next fraction; all other cases were accepted without suggestions. Conclusion: A training stepwise program was developed and successfully implemented to enable a therapist-driven workflow for online prostate MR-Linac adaptive radiotherapy.

Case Report: MR-Guided Adaptive Radiotherapy, Some Room to Maneuver.

Background: A magnetic resonance linear accelerator (MR-Linac) provides superior soft tissue contrast to evaluate inter- and intra-fraction motion and facilitate online adaptive radiation therapy (ART). We present here an unusual case of locally advanced castrate-resistant prostate cancer treated with high-dose palliative ultra-hypofractionated radiation therapy on the MR-Linac with significant inter-fraction tumor regression. Case Presentation: The patient was a 65-year-old man diagnosed with metastatic prostate cancer to bone and pelvic lymph nodes 7 years prior. At diagnosis, he presented with a PSA of 23 ng/ml and was commenced on a luteinizing hormone-releasing hormone agonist, achieving a PSA nadir of 4.68 ng/ml at 12 months. The patient subsequently had progressive lower urinary tract symptoms, his PSA increased to 47 ng/ml, and there was a markedly enlarged pelvic mass involving the prostate with gross extra-capsular disease and invasion into the posterior bladder wall. The patient was referred for palliative radiation to the pelvic mass due to urinary symptoms, pain, and lower limb paraesthesia. Treatment was planned to be delivered on the MR-Linac with a schedule of 36 Gy over 6 weekly factions allowing for maximal target dose delivery while minimizing surrounding organs at risk (OARs) radiation exposure. Unexpectedly, the target volume had a marked 49% (453 cc to 233 cc) reduction that was accounted for in the online adaptive process. A new reference plan was generated after 3 fractions to add sacral plexus as an OAR, previously not visible due to mass encroachment. The patient reported ongoing reduction in urinary symptoms, pelvic pain, and lower limb paresthesia by the end of treatment. Conclusion: Using daily MR-guided ART, improved visualization of the changing target and OARs ensured safe dose escalation. The unexpected positive response of the target and improved patient outcomes demonstrated the added value of the MR-Linac for online adaptive radiotherapy in this setting.

Pharmacokinetic Comparison of Chitosan-Derived and Biofermentation-Derived Glucosamine in Nutritional Supplement for Bone Health.

Glucosamine and chondroitin sulfate have been used as nutritional supplementation for joint tissues and osteoarthritis (OA). Biofermented glucosamine is of great interest in the supplement industry as an alternative source of glucosamine. The purpose of this study is to compare the pharmacokinetics of chitosan-derived glucosamine and biofermentation-derived glucosamine as nutritional supplementation. In a randomized, double-blind and cross-over study design, we recruited subjects of healthy men and women. The pharmacokinetics of glucosamine were examined after a single dose of glucosamine sulfate 2KCl (1500 mg) with two different sources of glucosamine (chitosan-derived glucosamine and biofermentation-derived glucosamine) to male and female subjects fitted with intravenous (iv) catheters for repeated blood sampling up to 8 h. According to plasma concentration-time curve of glucosamine after an oral administration of 1500 mg of glucosamine sulfate 2KCl, AUC0-8h and AUC0-∞ values of glucosamine following oral administration of chitosan-derived and biofermentation-derived glucosamine formulations were within the bioequivalence criteria (90% CI of ratios are within 0.8-1.25). The mean Cmax ratios for these two formulations (90% CI of 0.892-1.342) did not meet bioequivalence criteria due to high within-subject variability. There were no statistically significant effects of sequence, period, origin of glucosamine on pharmacokinetic parameters of glucosamine such as AUC0-8h, AUC0-∞, Cmax. Our findings suggest that biofermentation-derived glucosamine could be a sustainable source of raw materials for glucosamine supplement.

Impact of intrafraction changes in delivered dose of the day for prostate cancer patients treated with stereotactic body radiotherapy via MR-Linac.

Purpose: The purpose of this study is to evaluate the impact of intrafraction pelvic motion by comparing the adapted plan dose (APD) and the computed delivered dose of the day (DDOTD) for patients with prostate cancer (PCa) treated with SBRT on the MR-Linac. Methods: Twenty patients with PCa treated with MR-guided adaptive SBRT were included. A 9-field IMRT distribution was adapted based on the anatomy of the day to deliver a total prescription dose of 3000 cGy in 5 fractions to the prostate plus a 5 mm isotropic margin. Prostate, bladder, and rectum were re-contoured on the MR-image acquired during treatment delivery (MRBO). DDOTD was computed by propagating the dose from the daily adapted plan generated during treatment onto the MRBO. Results: Target coverage was met for all fractions, however, computed DDOTD was significantly less than the APD (p < 0.05). During an average treatment of 53 min, mean bladder volume increased by 116%, which led to a significant decrease in the DDOTD bladder D40% (p < 0.001). However, DDOTD to bladder 5 cc was significantly higher (p < 0.001) than APD. Rectum intrafraction changes were observed based on a volume change of -20% to 83% and presence of significant dose changes from APD to DDOTD for rectum D20% (p < 0.05) and D1cc (p < 0.0001). Conclusions: Intrafraction motion observed during prostate SBRT treatment on the MR-Linac have dosimetric impacts on both the target and organs at risk. Post-treatment computation using DDOTD may inform adaptation beyond anatomic changes in subsequent treatment fractions to best capitalize on MR-Linac technology and widen the therapeutic index of SBRT for PCa.

Dosimetric comparison of MR-guided adaptive IMRT versus 3DOF-VMAT for prostate stereotactic radiotherapy.

INTRODUCTION: To compare the dosimetry of prostate stereotactic radiotherapy (SBRT) delivered by adaptive intensity modulated radiotherapy (A-IMRT) and 3 degree of freedom volumetric modulated arc therapy (3DOF-VMAT). METHODS & MATERIALS: Twenty-five prostate patients treated with High Dose Rate (HDR) brachytherapy followed by SBRT were included (fifteen with hydrogel spacer in place for treatment). Interfraction changes in the volume of prostate, rectum and bladder were measured. Fractional dose to these structures was estimated for A-IMRT and 3DOF-VMAT for comparison against the corresponding reference dose and between each other. RESULTS: Clinically acceptable dose was delivered to prostate in all 125 fractions through A-IMRT and 3DOF-VMAT. A-IMRT was better than 3DOF-VMAT in reducing dose to 1 cm3 of rectum. Conversely, 3DOF-VMAT was superior in sparing 50% and 20% of rectum. When comparing the reference and delivered dose, there was no significant difference for Bladder D5cm3 for either technique. However, rectum in the high dose region benefited more from A-IMRT by being irradiated to a lower than reference dose in more fractions than 3DOF-VMAT. Hydrogel spacer reduced the rectal dose and was associated with a smaller deviation from reference dose for rectum D50% for A-IMRT. CONCLUSIONS: Despite the presence of large interfraction organ volumes changes, clinically acceptable dose was delivered to the prostate by both systems. A-IMRT facilitated a greater rectal sparing from the high dose region than 3DOF-VMAT. Further reduction in rectal dose could be achieved by hydrogel spacer to displace the rectum, or by adaptation delivered by VMAT.

Respiratory Volume Monitoring in the Perioperative Setting Across Multiple Centers.

BACKGROUND: The prevalence of nuisance (technical) alarms is the leading cause of alarm fatigue resulting in decreased awareness and a reduction in effective care. The Joint Commission identified in their National Patient Safety goals alarm fatigue as a major safety issue. The introduction of noninvasive respiratory volume monitoring (RVM) has implications for effective perioperative respiratory status management. We evaluated this within the Kaiser Permanente health system. METHODS: This observational study was conducted at 4 hospitals in the Kaiser Permanente system. Standard data from RVM, pulse oximetry, and capnography were collected postoperatively in the post-anesthesia care unit (PACU) and/or on the general hospital floor. Device-specific alarm types, rates, and respective actions were recorded and analyzed by non-study staff. RESULTS: RVM was applied to 247 subjects (143 females, body mass index 32.3 ± 8.7 kg/m2, age 60.9 ± 13.9 y) providing 2,321 h. RVM alarms occurred 605 times (0.25 alarms/h); 64% were actionable and addressed, 17% were not addressed, 13% were self-resolved, and only 6% were nuisance. In a subgroup, RVM completed all 127 h of monitoring, whereas oximetry with capnography only completed 51 h with 12.9 alarms/h (73% nuisance). The overall RVM alarm rate was significantly lower than with either pulse oximeters or capnography monitors. We saw a nearly 1,000-fold reduction in nuisance alarms compared to capnography and a 20-50-fold reduction in nuisance alarms compared to pulse oximetry. CONCLUSIONS: Our study indicates that alarm fatigue due to nuisance alarms continues to be a clinical challenge in perioperative settings. Among the 3 common technologies for respiratory function monitoring, RVM had the lowest rate of overall technical alarms and the highest rate of compliance. Furthermore, with early interventions, none of the subjects monitored with RVM suffered any negative outcomes.

Intracranial Germ Cell Tumors in Adolescents and Young Adults: A 40-Year Multi-Institutional Review of Outcomes.

PURPOSE: The aim of this study was to determine the practice patterns and outcomes of intracranial germ cell tumors (IGCT) in adolescents and young adults according to different therapeutic approaches. METHODS AND MATERIALS: One-hundred twelve patients with IGCT aged 15 to 39 years were managed at either XX or the XY center from 1975 to 2015. The charts were retrospectively reviewed and data collected. RESULTS: Median duration of follow-up was 8.3 years. Ninety-four patients had germinomas, and 18 had nongerminomatous germ cell tumors (NGGCT). The primary disease sites were pineal gland (37 of 94 germinoma, 14 of 18 NGGCT) and suprasellar region (23 of 94 germinoma, 2 of 18 NGGCT). Eleven patients with germinoma (12%) and 2 patients with NGGCT (11%) had radiographic spinal metastases or positive lumbar cerebrospinal fluid cytology. Event-free survival (EFS) was 84% and overall survival (OS) was 90% at 10 years for germinoma; EFS was 71% and OS was 86% at 10 years for NGGCT. For patients with germinoma, 10-year EFS was 100% after craniospinal radiation therapy (CSRT) with chemotherapy (N = 10); 100% after whole-ventricular radiation therapy (WVRT), whole-brain radiation therapy (WBRT), or focal radiation therapy (FRT) with chemotherapy (N = 22); 90% after CSRT alone (N = 46); and 41% after WVRT, WBRT, or FRT alone (N = 16) (P < .0005). Ten-year OS was 100%, 100%, 90%, and 72%, respectively (P = .032). For patients with NGGCT, 10-year EFS was 80% after CSRT, WBRT, or WVRT plus chemotherapy (N = 10) versus 58% after FRT plus chemotherapy (N = 8) (P = .31); 10-year OS was 90% versus 58%, respectively (P = .16). CONCLUSIONS: We report excellent overall outcomes according to treatment approach in the largest study of IGCT in adolescents and young adults to our knowledge. EFS and OS were inferior after non-CSRT without chemotherapy in germinoma.

Treatment of objective tinnitus with transpalatal Botox® injection in a pediatric patient with middle ear myoclonus: A case report.

We describe a case of bilateral middle ear myoclonus (MEM) that was treated with trans-palatal Botox® injection after failing surgery to section the tensor tympani and stapedial tendons. MEM is a rare disorder resulting from rhythmic contraction of middle ear muscles. An 8-year old girl presented with audible clicking tinnitus, and resultant inability to focus in school. Her parents declined medical therapy, and she underwent surgeries for tendon lysis, with only temporary relief. She had successful response to trans-palatal Botox® injection to the tensor veli palatini aponeurosis. Trans-palatal Botox® injection is a safe and reasonable alternative for treatment of MEM.

Anticoagulation and antiplatelet therapy in awake transcervical injection laryngoplasty.

OBJECTIVE: Vocal fold movement impairment (VFMI) due to neuronal injury occurs in 20% to 30% of surgeries in the region of the aortic arch. Early injection laryngoplasty can aid with postoperative pulmonary toilet in these high-risk cardiovascular patients. The purpose of this study is to determine whether continuing antiplatelet and anticoagulation therapy during awake transcervical injection laryngoplasty surgery is safe, and if there is any increase in bleeding complications in these patients. METHODS: This is a retrospective review of patients undergoing awake injection laryngoplasty surgery for VFMI between 2013 and 2016 at a tertiary academic center specializing in aortic and mediastinal diseases. Records were reviewed for patients regarding baseline antiplatelet or anticoagulation therapy, and whether these medications were stopped or continued preoperatively. The primary outcome was bleeding complications. RESULTS: Of the 95 surgeries reviewed, 44 (46%) were performed for patients on antiplatelet therapy, and 71 (75%) for patients on anticoagulation therapy. None of the patients on antiplatelet therapy had their treatment discontinued. Of the patients on anticoagulation, 13 (16.4%) had their therapy held prior to surgery. There was no observed difference in bleeding complications between patients who were continued on antiplatelet or anticoagulation treatment versus those whose therapy was withheld. CONCLUSION: These results suggest that patients undergoing awake transcervical injection laryngoplasty for VFMI can be maintained on antiplatelet or anticoagulation therapy without increased risk of bleeding. Further larger studies are needed to confirm these findings. LEVEL OF EVIDENCE: 4. Laryngoscope, 127:1850-1854, 2017.

What's in a Prerequisite? A Mixed-Methods Approach to Identifying the Impact of a Prerequisite Course.

Despite the ubiquity of prerequisites in undergraduate science, technology, engineering, and mathematics curricula, there has been minimal effort to assess their value in a data-driven manner. Using both quantitative and qualitative data, we examined the impact of prerequisites in the context of a microbiology lecture and lab course pairing. Through interviews and an online survey, students highlighted a number of positive attributes of prerequisites, including their role in knowledge acquisition, along with negative impacts, such as perhaps needlessly increasing time to degree and adding to the cost of education. We also identified a number of reasons why individuals do or do not enroll in prerequisite courses, many of which were not related to student learning. In our particular curriculum, students did not believe the microbiology lecture course impacted success in the lab, which agrees with our analysis of lab course performance using a previously established "familiarity" scale. These conclusions highlight the importance of soliciting and analyzing student feedback, and triangulating these data with quantitative performance metrics to assess the state of science, technology, engineering, and mathematics curricula.

A Familiar(ity) Problem: Assessing the Impact of Prerequisites and Content Familiarity on Student Learning.

Prerequisites are embedded in most STEM curricula. However, the assumption that the content presented in these courses will improve learning in later courses has not been verified. Because a direct comparison of performance between students with and without required prerequisites is logistically difficult to arrange in a randomized fashion, we developed a novel familiarity scale, and used this to determine whether concepts introduced in a prerequisite course improved student learning in a later course (in two biology disciplines). Exam questions in the latter courses were classified into three categories, based on the degree to which the tested concept had been taught in the prerequisite course. If content familiarity mattered, it would be expected that exam scores on topics covered in the prerequisite would be higher than scores on novel topics. We found this to be partially true for "Very Familiar" questions (concepts covered in depth in the prerequisite). However, scores for concepts only briefly discussed in the prerequisite ("Familiar") were indistinguishable from performance on topics that were "Not Familiar" (concepts only taught in the later course). These results imply that merely "covering" topics in a prerequisite course does not result in improved future performance, and that some topics may be able to removed from a course thereby freeing up class time. Our results may therefore support the implementation of student-centered teaching methods such as active learning, as the time-intensive nature of active learning has been cited as a barrier to its adoption. In addition, we propose that our familiarity system could be broadly utilized to aid in the assessment of the effectiveness of prerequisites.

Development of a robust DNA quality and quantity assessment qPCR assay for targeted next-generation sequencing library preparation.

Next-generation sequencing (NGS) is becoming a standard for genetic analyses of clinical samples. DNAs retrieved from formalin-fixed, paraffin-embedded (FFPE) tissue specimens are commonly degraded, and specimens such as core biopsies are sometimes too small to obtain enough DNA for NGS applications. Thus, it is important to measure both the DNA quantity and quality accurately from clinical samples. However, there is no standard method for DNA quantity and quality analyses for NGS library preparation. We tested four different methods (PicoGreen, Qubit® fluorometry, TaqMan and SYBR-Green-based qPCR assay) and compared each to RNase P TaqMan as a reference control. We found that SYBR-Green-based qPCR assay provides a consistent and accurate DNA quantification while keeping its cost relatively low and the throughput high. We designed a dual-probe SYBR-Green qPCR assay for DNA quantity and quality assessment for targeted NGS library preparation. This assay provides a Dscore (degradation score) of the interrogated DNA by analyzing two different sizes of amplicons. We show an example of a clinical sample with a very high Dscore (high degradation). With a regular DNA quantification, without considering the degradation status, no correct NGS libraries were obtained. However, after optimizing the library condition by considering its poor DNA quality, a reasonably good library and sequencing results were obtained. In summary, we developed and presented a new DNA quantity and quality analysis qPCR assay for the targeted NGS library preparation. This assay may be mostly efficient for the clinical samples with high degradation and poor DNA quality.

Comprehensive evaluation and validation of targeted next-generation sequencing performance in two clinical laboratories.

Next-generation sequencing (NGS) has led to breakthroughs for genetic and genomic analyses and personalized medicine approaches for many diseases. More and more clinical laboratories are using NGS as a genetic screening tool for providing mutation information that is used to select the best treatment regimens for cancer patients. However, several obstacles prevent the routine implementation of NGS technology into the clinical molecular diagnosis setting: the sophisticated sample preparation process, high cost, time-consuming data analyses, as well as the reproducibility and accuracy of interpretation. To systematically evaluate the performance and quality of targeted NGS cancer panel analyses in clinical laboratories, we performed three different tests: i) laboratory-to-laboratory accuracy test, ii) intra-laboratory precision validation, and iii) limit of detection test, using formalin-fixed, paraffin-embedded cancer tissue specimens, cell lines and mutation positive DNA. A laboratory-to-laboratory accuracy test performed using 51 samples showed 100% sensitivity and 99.97% specificity. For the intra-laboratory precision test, 100% reproducibility was observed. For the limit of detection test, KRAS mutations from samples diluted from 70 to 2% of mutant allele frequencies were detected correctly. We believe that the present study demonstrated the feasibility of clinical implementation of a targeted NGS cancer panel analysis for personalized medicine.