Modified SureSelectQXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples

Background

Personalised medicine is nowadays a major objective in oncology. Molecular characterization of tumours through NGS offers the possibility to find possible therapeutic targets in a time- and cost-effective way. However, the low quality and complexity of FFPE DNA samples bring a series of disadvantages for massive parallel sequencing techniques compared to high-quality DNA samples (from blood cells, cell cultures, etc.).

Results

We performed several experiments to understand the behaviour of FFPE DNA samples during the construction of SureSelect^QXT libraries. First, we designed a quality checkpoint for FFPE DNA samples based on the quantification of their amplification capability (qcPCR). We observed that FFPE DNA samples can be classified according to DIN value and qcPCR concentration into unusable, or low-quality (LQ) and good-quality (GQ) DNA. For GQ samples, we increased the amount of input DNA to 150 ng and the digestion time to 30 min, whereas for LQ samples, we used 50 ng of DNA as input but we decreased the digestion time to 1 min. In all cases, we increased the cycles of the pre-hyb PCR to 10 but decreased the cycles of the post-hyb PCR to 8. In addition, we confirmed that using half of the volume of reagents can be beneficial. Finally, in order to obtain better results, we designed a decision flow-chart to achieve a seeding concentration of 12–14 pM for MiSeq Reagent Kit v2.

Conclusions

Our experiments allowed us to unveil the behaviour of low-quality FFPE DNA samples during the construction of SureSelect^QXT libraries. Sequencing results showed that, using our modified SureSelect^QXT protocol, the final percentage of usable reads for low-quality samples was increased more than three times allowing to reach median depth/million reads values of 76.35. This value is equivalent to ~ 0.9 and ~ 0.7 of the values obtained for good-quality FFPE and high-quality DNA respectively.

Electronic supplementary material

The online version of this article (10.1186/s12575-018-0084-7) contains supplementary material, which is available to authorized users.

Validity of automated refraction after segmented refractive multifocal intraocular lens implantation

AIM

To evaluate the clinical utility of automated refraction (AR) and keratometry (KR) compared with subjective or manifest refraction (MR) after cataract or refractive lens exchange surgery with implantation of Lentis Mplus X (Oculentis GmbH) refractive multifocal intraocular lens (IOL).

METHODS

Eighty-six eyes implanted with the Lentis Mplus X multifocal IOL were included. MR was performed in all patients followed by three consecutive AR measurements using the Topcon KR-8000 autorefractor. Assessment of repeatability of consecutive AR before and after dilation with phenylephrine 10%, and comparison of the AR and KR with MR using vector analysis were performed at 3mo follow-up.

RESULTS

Analysis showed excellent repeatability of the AR measurements. Linear regression of AR versus MR showed good correlation for sphere and spherical equivalent, whereas the correlation for astigmatism was low. The mean difference AR-MR was -1.28±0.29 diopters (D) for sphere. Astigmatism showed better correlation between KR and MR.

CONCLUSION

We suggest AR sphere plus 1.25 D and the KR cylinder as the starting point for MR in eyes with a Lentis Mplus X multifocal IOL. If AR measurements are equal to MR, decentration of the IOL should be suspected.

Safety and Efficacy of the Transition from Extracapsular Cataract Extraction to Manual Small Incision Cataract Surgery in Prevention of Blindness Campaigns

PURPOSE

To compare the safety and the visual outcomes of two experienced cataract surgeons who converted from extracapsular cataract extraction (ECCE) to manual small incision cataract surgery (MSICS) during a campaign for the prevention of blindness.

METHODS

Two surgeons used the ECCE technique (ECCE group) during a campaign in Burkina Faso on 93 consecutive cataract patients with a corrected distance visual acuity (CDVA) <20/80 in the best eye. Both surgeons used MSICS for the first time on 98 consecutive cases in another campaign in Kenya after theoretical instructional courses.

RESULTS

There were no significant differences in CDVA at 3 months postoperatively. There were 69% of eyes with uncorrected distance visual acuity ≥20/60 in the MSICS group and 49% eyes in the ECCE group. Spherical equivalents ranged between -1D and +1D in 55% of the MSICS group versus 43% in the ECCE group. There were significant differences in the changes in the vertical component of astigmatism (J45) but not the horizontal (J0) component. There were no significant differences in the intraoperative complications. The most common postoperative complication was corneal edema on the first day in 40.86% and 19.38% of the ECCE and MSICS groups, respectively.

CONCLUSION

Transitioning from ECCE to MSICS for experienced cataract surgeons in surgical campaigns is safe. The rate of complications is similar for both techniques. Slightly better visual and refractive outcomes can be achieved due to the decreased induction of corneal astigmatism.

Prevalence and location of the secondary mesiobuccal canal in 1,100 maxillary molars using cone beam computed tomography

BACKGROUND

Several articles have used cone beam computed tomography (CBCT) to study the morphology of the maxillary molars and to ascertain its ability to visualize the second mesiobuccal canal (MB2); however, its geometric location has not been examined in depth. The aim of this study was to describe in vivo the prevalence and location of the MB2 in the mesiobuccal root of the first maxillary molar (1MM) and the second maxillary molar (2MM) through CBCT imaging.

METHODS

Five hundred fifty CBCT images of the 1MM and 550 of the 2MM were analyzed. To detect the MB2 canal, the observation and measurements were done 1 mm apically to the pulpal floor to standardize the methodology. The geometric location of the central point of the MB2 canal (PMB2) was measured in relation to the central point of the mesiobuccal canal (PMB1) and in relation to the line projected between the PMB1 and the central point of the palatal canals (PP). The data were analyzed using descriptive statistics, with a value of P < 0.05 being statistically significant.

RESULTS

In the 1MM, the prevalence of the MB2 canal was 69.82% and was more frequent in women (p = 0.005). The distance between PMB1 and PP was 7.64 ± 1.04 mm. The average distance between PMB1 and PMB2 was 2.68 ± 0.49 mm, and for PMB2 and the line projected between the PMB1 and PP canals was 1.25 ± 0.34 mm. In the 2MM, the MB2 canal was identified in 46.91% and was more frequent in men (p = 0.000). The distance between PMB1 and PP was 7.02 ± 1.30. The average distance between PMB1 and PMB2 was 2.41 ± 0.64 mm, and for the PMB2 and the line projected between the PMB1 and PP canals was 0.98 ± 0.33 mm.

CONCLUSIONS

The MB2 canal was found in a high percentage of the sample. These results indicate that CBCT is an effective, high-precision diagnostic tool not only for detecting but also locating in vivo the MB2 canal in the mesiobuccal root of upper molars.

Molecular genetic heterogeneity in undifferentiated endometrial carcinomas

Undifferentiated and dedifferentiated endometrial carcinomas are rare and highly aggressive subtypes of uterine cancer, not well characterized at a molecular level. To investigate whether dedifferentiated carcinomas carry molecular genetic alterations similar to those of pure undifferentiated carcinomas, and to gain insight into the pathogenesis of these tumors, we selected a cohort of 18 undifferentiated endometrial carcinomas, 8 of them with a well-differentiated endometrioid carcinoma component (dedifferentiated endometrioid carcinomas), and studied them by immunohistochemistry and massive parallel and Sanger sequencing. Whole-exome sequencing of the endometrioid and undifferentiated components, as well as normal myometrium, was also carried out in one case. According to The Cancer Genome Atlas classification, we distributed 95% of the undifferentiated carcinomas in this series as follows: (a) hypermutated tumors with loss of any mismatch repair protein expression and microsatellite instability (eight cases, 45%); (b) ultramutated carcinomas carrying mutations in the exonuclease domain of POLE (two cases, 11%); (c) high copy number alterations (copy-number high) tumors group exhibiting only TP53 mutations and high number of alterations detected by FISH (two cases, 11%); and (d) low copy number alterations (copy-number low) tumors with molecular alterations typical of endometrioid endometrial carcinomas (five cases, 28%). Two of the latter cases, however, also had TP53 mutations and higher number of alterations detected by FISH and could have progressed to a copy-number high phenotype. Most dedifferentiated carcinomas belonged to the hypermutated group, whereas pure undifferentiated carcinomas shared molecular genetic alterations with copy-number low or copy-number high tumors. These results indicate that undifferentiated and dedifferentiated endometrial carcinomas are molecularly heterogeneous tumors, which may have prognostic value.

Implantable Collamer Lens for Myopia: Assessment 12 Years After Implantation

PURPOSE

To evaluate the long-term refractive and visual stability and the risks related to the implantation of Implantable Collamer Lens (ICL; STAAR Surgical, Monrovia, CA) phakic intraocular lens (PIOL) for myopia.

METHODS

This retrospective, consecutive, cumulative clinical study was performed in a group of 144 eyes implanted with ICL PIOL for myopia. Only the cases with clinical data available 12 years after the implantation were included in the series. Corrected distance visual acuity (CDVA), uncorrected distance visual acuity, spherical equivalent, refractive astigmatism, endothelial cell density, ICL vaulting, and postoperative complications were analyzed.

RESULTS

Mean spherical equivalent refraction was -16.90±4.26 diopters (D) preoperatively and -1.77±1.93 D 12 years postoperatively. Mean CDVA at the first and last visit were 0.31±0.19 logMAR and 0.22±0.22 logMAR, respectively (Mann-Whitney U test, P<.001). Twelve years postoperatively, 8.9% of eyes had lost more than two lines of CDVA. The incidence of clinically relevant cataracts (13.88%) was significantly linked to the use of the V3 model ICL (chi-square test, P=.007). During the follow-up period, a significant reduction in PIOL vaulting was observed (Kruskal-Wallis test, P<.05), and the mean endothelial cell density decreased by 19.75%.

CONCLUSIONS

The ICL PIOL provided good refractive outcomes and stability in the long term. The incidence of cataracts is low when the latest models of this PIOL are used.

Simultaneous topography-guided partial photorefractive keratectomy and corneal collagen crosslinking for keratoconus

PURPOSE

To report the visual, refractive, and clinical outcomes of simultaneous topography-guided partial photorefractive keratectomy (PRK) and corneal collagen crosslinking (CXL) in eyes with keratoconus.

SETTING

Private practice surgery center, Dubai, United Arab Emirates.

DESIGN

Retrospective cohort study.

METHODS

Refraction, uncorrected (UDVA) and corrected (CDVA) distance visual acuities, flat and steep keratometry (K) readings, and complications were evaluated 1, 3, 6, and 12 months postoperatively.

RESULTS

The study enrolled 31 eyes of 31 patients aged 21 to 42 years. All study parameters showed a statistically significant improvement at 3, 6, and 12 months over baseline values. At 12 months, the mean UDVA improved to 0.23 logMAR±0.33 (SD) from 0.79±0.36 logMAR (P<.001) and the CDVA improved to 0.06±0.07 logMAR from 0.28±0.20 logMAR (P<.001). The mean defocus decreased from 3.45±1.60 diopters (D) to 1.88±1.58 D (P<.001). The flat K and steep K readings showed significant flattening. The mean refractive astigmatism decreased from -2.77±1.47 D to -0.98±0.76 D (P<.001). The improvement in study parameters plateaued after 3 months.

CONCLUSION

Simultaneous topography-guided partial PRK and CXL was effective, safe, and stable in keratoconus patients.

FINANCIAL DISCLOSURE

No author has a financial or proprietary interest in any material or method mentioned.

TMJ in facial class III deformity. Condylar morphology relations

Class III dentofacial deformities (DF-III) are classified as a severe functional and esthetic anomaly. This work aims to describe the condylar morphology of subjects with DF-III and indication of correction through orthognatic surgery. A descriptive study was designed in the Division of Oral and Maxillofacial Surgery of the Universidad de La Frontera, Chile, where 14 patients were examined with conventional cephalometric studies to determine the surgical indication; then, cone beam CT images were recorded for the morphometric analyses on the coronal and axial slices, considering linear measurements in the middle, basal and anteroposterior areas. The data were analyzed with the student's t-test, considering p < 0.05 statistically significant. The results revealed condylar size differences of less than 1 mm between the left and right condyles, considering average widths of 17.03 mm in the right condyle and 17.86 mm in the left condyle. Vertically, the observed averages were 17.17 mm in the right condyle and 17.04 mm in the left condyle; no statistical differences were observed. It can be concluded that there are no differences in the measurements when the two condyles are compared in this type of subject.

TMJ in facial class III deformity. Condyle/fossa relations

The aim of this study was to ascertain the joint space present in the TMJ of subjects diagnosed with Class III dentofacial deformity with an indication for orthognathic surgery. Fourteen subjects were recruited from the Division of Oral and Maxillofacial Surgery at the Universidad de La Frontera, Chile. All subjects were admitted to the study after signing an informed consent and undergoing cephalometric analyses to define the severity of the deformity. Then, the joint space was analyzed, studying a cone beam CT image of the TMJ, which was evaluated in the coronal and sagittal views, defining the most anterior, median and posterior joint space (sagittal view), as well as the lateral, median and medial joint space (coronal view). The data were recorded in millimeters by an observer and data were analyzed after measuring the same parameter at three different times. A student's t-test was used for the analyses. Differences observed in both joints were not greater than 0.2 mm with spaces between 2 mm and 1.5 mm, thereby establishing the homogeneity of the sample, which presented no significant differences between the two joint spaces (right and left). It can be concluded that the joint space is symmetrical in both condyles and that no important changes are present compared to the results indicated in the international literature.

Ancillary personnel in Spanish and Latin-American hospitals faced with living related kidney donation

INTRODUCTION

Ancillary hospital personnel represent an important body of opinion because as they work in a hospital their opinion has more credibility for the general public as a result of their activity in hospitals. However, in most cases they do not have any health care training which means that their attitude could be based on a lack of knowledge or unfounded fears.

OBJECTIVE

To analyze the attitude toward living kidney donation (LKD) among ancillary personnel in Spanish and Latin-American hospitals and to analyze the variables that might influence such attitude.

PATIENTS AND METHOD

from «International Collaborative Donor Project» a random sample was taken among ancillary personnel in Spain, Mexico and Cuba hospitals. Attitude towards LKD was evaluated using a validated, anonymously filled and self-administered survey.

RESULTS

951 professionals were surveyed (Spain: 277, Mexico: 632, Cuba: 42). 89% (n=850) are in favor of related kidney donation, lowering to 31% (n=289) in non-related donation. Of the rest, 8% (n=78) are not in favor and the 3% (n=23) are unsure. By country, Cubans (98%) and Mexicans (91%) are more in favour than Spanish (84%) (P=.001). The following variables are related to favourable attitude towards LKD: female sex (P=.017), university degree (P=.010), work in health services (P=.035), labour stability (P=.016), personal experience in donation and transplantation (P=.001), positive attitude toward cadaveric donation (P<.001), belief that he or she might need a transplant in the future (P<.001), positive attitude towards living liver donation (P<.001), a willingness to receive a donated living liver if needed (P<.001), having discussed the subject of organ donation and transplantation within the family (P<.001), partner's positive attitude towards the subject (P<.001), participation in voluntary type pro-social activities (P=.002) and not being concerned about possible mutilation after donation (P<.001) CONCLUSIONS: The attitude toward living related kidney donation is favourable among ancillary personnel in Spanish and Latin-Americans hospitals. Because living donation is a better source of organs than cadaveric ones, this favourable predisposition can be used as promoting agent of living donation in order to develop it in Spanish-speaking countries.

Add-on sulcus-based versus primary in-the-bag multifocal intraocular lens: intraindividual study

PURPOSE

To compare the clinical outcomes of add-on sulcus-based multifocal and standard in-the-bag multifocal intraocular lens (IOL) implantation.

METHODS

Twenty-one patients with unilateral monofocal pseudophakia underwent add-on sulcus-based Acri. LISA 536D multifocal IOL (Carl Zeiss Meditec, Jena, Germany) implantation (add-on multifocal IOL group) and contralateral phacoemulsification with in-the-bag Acri.LISA 376D multifocal IOL (Carl Zeiss Meditec) implantation (primary multifocal IOL group). Uncorrected distance visual acuity, uncorrected near visual acuity, corrected distance visual acuity, distance-corrected near visual acuity, photopic (90 cd/m(2)) distance, near contrast sensitivity, mesopic (5 cd/m(2)) distance contrast sensitivity with and without glare, wavefront aberrations, and complications were measured 6 months postoperatively.

RESULTS

Primary in-the-bag multifocal IOLs provided slightly but significantly better uncorrected distance visual acuity (0.08 ± 0.10 vs 0.17 ± 0.15 logMAR, P = .028), uncorrected near visual acuity (0.09 ± 0.17 vs 0.18 ± 0.11 logMAR, P = .005), and corrected distance visual acuity (0.01 ± 0.04 vs 0.04 ± 0.05 logMAR, P = .038). There were no significant differences in distance-corrected near visual acuity, photopic or mesopic contrast sensitivity under different conditions, and wavefront aberrations. Complications included pigment dispersion in one eye (4.8%) and pupillary capture in 2 eyes (9.5%) of the add-on multifocal IOL group.

CONCLUSIONS

The secondary add-on sulcus-based multifocal IOL provided useful pseudoaccommodation with vision quality similar to the primary in-the-bag multifocal IOL. The technique should be considered in patients diagnosed as having unilateral or bilateral monofocal pseudophakia seeking near spectacle independence.

Ibuprofen inhibits the synaptic failure induced by the amyloid-β peptide in hippocampal neurons

Epidemiological studies have reported a decrease in the prevalence of Alzheimer's disease in individuals who chronically use non-steroidal anti-inflammatory drugs (NSAIDs). Clinical trials, on the other hand, have been less positive. Nevertheless, it has been proposed that NSAIDs exert part of their effects by reducing long-term cerebral neuroinflammation, although this mechanism has not been proven. In this study, we report that ibuprofen, one of the more widely used non-steroidal anti-inflammatory drugs, was able to alter the ultrastructure of amyloid-β peptide (Aβ) and significantly decrease its association to neuronal membranes, and consequently, its synaptotoxic effect in rat primary hippocampal and cortical cultures at 24 h incubation. In agreement with these results, we found that the decrease in the frequency of calcium transients with Aβ was partly recovered by addition of ibuprofen (8.0 × 10-2 Hz in control; 3.4 × 10-2 Hz in 5 μM Aβ, and 5.9 × 10-2 Hz in the presence of Aβ and 200 μM ibuprofen). Additionally, this effect correlated well with the increment and recovery of miniature spontaneous currents (47 ± 5% of control in 1 μM Aβ alone and 104 ± 14% in the presence of Aβ and ibuprofen). Our results suggest that ibuprofen could be exerting its neuroprotective effect by directly interacting with Aβ and altering its toxic aggregated forms. We postulate that other ibuprofen analogs with better pharmacological properties might have a higher efficacy in AD.

Effect of platelet-rich plasma in nerve regeneration after LASIK

PURPOSE

To investigate the effect of topical eye application of platelet-rich plasma (E-PRP) on the recovery of corneal sensitivity after LASIK and the anatomical recovery of the sub-basal corneal plexus as studied by confocal microscopy.

METHODS

This was a randomized, consecutive, controlled, prospective and masked study on 108 myopic eyes receiving LASIK. The main variables of the study were the increase in corneal sensitivity (Cochet-Bonet aesthesiometer; Luneau, Paris, France) and the aspect of the sub-basal nerve plexus (confocal microscope). Additionally, a biomicroscopic study of the epithelial status of the cornea and a subjective questionnaire were completed. Each eye of each patient was assigned to one of two groups: 54 eyes treated with balanced saline solution and 54 fellow eyes receiving PRP drops for 3 months.

RESULTS

No significant differences were detected when the corneal sensitivity thresholds were compared at any postoperative visit in both groups (P > .05 for all comparisons). Almost identical sub-basal fiber densities were estimated for both groups before LASIK (t test, P = .66). However, the type and severity of staining detected during the slit-lamp examinations at the first and third month postoperatively were significantly less evident in the E-PRP treatment group (Wilcoxon test, P < .05).

CONCLUSIONS

PRP drops have beneficial effects for promoting epithelial status after LASIK but have no positive effect on recovery of corneal sensitivity, probably due to the limited bioavailability of growth factors in corneal stroma when the substance is topically administered.

Multivariate analysis to determine the factors affecting the attitudes toward organ donation of healthcare assistants in Spanish and Mexican healthcare centers

BACKGROUND

Healthcare assistants are an important group of workers who can influence public opinion. Their attitudes toward organ donation may influence public awareness of healthcare matters; negative attitudes toward donation and transplantation could have a negative impact on public attitudes. Our objective was analyze the attitudes of healthcare assistants, in Spanish and Mexican healthcare centers toward organ donation and determine factors affecting them using a multivariate analysis.

MATERIAL AND METHODS

As part of the "International Collaborative Donor Project," 32 primary care centers and 4 hospitals were selected in Spain and 5 hospitals in Mexico. A randomized sample of healthcare assistants was stratified according to healthcare services. Attitudes were evaluated using a validated questionnaire of the psychosocial aspects of donation, which was self-completed anonymously by the respondent. Statistical analysis used the chi-square test, Student t test, and logistic regression analysis.

RESULTS

Of 532 respondents, 66% in favored donation and 34% were against it or undecided. Upon multivariate analysis, the following variables had the most weight: 1) country of origin (Mexicans were more in favor than Spanish; odds ratio [OR]) = 1.964; P = .014); 2) a partner with a favorable attitude (OR = 2.597; P = .013); 3) not being concerned about possible bodily mutilation after donation (OR = 2.631; P = .006); 4) preference for options apart from burial for handling the body after death (OR = 4.694; P < .001) and 5) accepting an autopsy if one was needed (OR = 3.584; P < .001).

CONCLUSIONS

The attitudes of healthcare assistants toward organ donation varied considerably according to the respondent's country of origin. The psycho-social profile of a person with a positive attitude to donation was similar to that described within the general public.