Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests

The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of melanoma FFPE samples for an amplicon-based NGS custom panel analysis. DNA was extracted from unstained melanoma samples and wide local excision samples. Amplicon-based libraries were constructed and tested using time and quality parameters as variables. Time elapsed from sample retrieval >7 years, a quality control value > 5.63 and a DNA integrity value < 2.05 indicated samples were not suitable. A decision tree is provided with rate of samples suitable for analysis according to the combination of these parametersThis study has been funded by the Instituto de Salud Carlos III grant number PI15/01860, the Junta Provincial de Valencia de la Asociación Española contra el Cancer through a PhD grant, and by the Universidad Católica de Valencia San Vicente Mártir. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscrip

Sonochemical oxidation of technical lignin to obtain nanoparticles with enhanced functionality

Kraft lignin (KL) was treated by employing mild oxidation conditions enhanced by ultrasound irradiation (US) for obtaining more functionalized particles, avoiding the undesired side reactions of degradation and depolymerization. The aim was to obtain products with plausible value for applications with a greater potential market, enabling the introduction of low-cost bio-based materials for technically advanced applications. In the present work, KL was oxidized in alkaline media, applying low temperatures (30–60 °C), short times (15 to 60 min), and US waves (20 kHz). The influence of incorporating hydrogen peroxide (H2O2) as an oxidizing agent was also studied, as well as the chemical composition, physicochemical, thermal, and morphological properties of the final lignin particles. It was observed from Quantitative Acid Hydrolysis (QAH), Elemental Analysis (EA), and molecular weights (Mw) that oxidized lignin particles (OxL) did not suffer any major degradation. Other techniques used to determine physicochemical properties, such as Fourier Transformed Infrared (FTIR), 31 Phosphorous Nuclear Magnetic Resonance (31P NMR), or Ultraviolet–visible (UV-vis) methods, corroborated oxidation reactions, evident by the increment of carboxylic groups. The most noticeable difference, however, was observed when the stability and morphology of the particles were observed by Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM). Some conditions greatly promoted the formation of more stable and nanosized particles. The best conditions were the mildest but with the highest reaction times (no addition of H2O2, 30 °C and 60 minutes). Moreover, all reactions had good recovery yields, above 70% of the original lignin.The authors would like to acknowledge the Basque Government for the financial support of this research through project IT1498-22 and grant PIF19-183. E. R. wants to acknowledge the tenure track position “BOIS” part of E2S UPPA supported by the “Investissements d'Avenir” French program managed by ANR (ANR-16-IDEX-0002). The authors thank for the technical and human support provided by SGIker (UPV/EHU/ERDF, EU)

Informing patients about their mutation tests : CDKN2A c.256G>A in melanoma as an example

Background When germline mutations are suspected as causal in cancer, patient DNA may be sequenced to detect variants in relevant genes. If a particular mutation has not been reported in reliable family studies, genetic counselors are facing a dilemma of appropriately informing patients. Many sequencing facilities provide an interpretation of the findings based on the available sequence databases or on prediction tools that are curated from bioinformatics and mechanistic datasets. The counseling dilemma is exacerbated if the pedigree data are not informative but the in silico predictions suggest pathogenicity. Methods We present here a real world example of the c.256G > ACDKN2Avariant, which was detected in one melanoma patient where two siblings were diagnosed with melanoma in situ. We investigated a detailed family history of the affected siblings in order to survey probability of the cancer risks within the context to this mutation. Results This c.256G > ACDKN2Avariant was detected in one of the brothers and in the melanoma-free mother while the other brother in the family tested negative. The variant had been previously described in one patient from a melanoma family. In the family under investigation, the mother's 16 first-and second-degree relatives had survived past the median onset age for melanoma and none presented melanoma. We tested the variant using multiple bioinformatic tools that all predicted deleteriousness of the variant. The genetic counseling report to the melanoma patient stated that theCDKN2Avariant was 'likely pathogenic' and the disease was defined as 'likely hereditary melanoma'. Conclusions The pedigree data showed at the most a low penetrance variant, which, if taken into consideration, might have altered the provided diagnosis. When dealing with 'practically' unknown variants the counselors would be advised to incorporate a detailed family history rather than basing predictions on functionality provided by sequencing facilities.Peer reviewe

Assessment of Bleached and Unbleached Nanofibers from Pistachio Shells for Nanopaper Making

Cellulose and lignocellulose nanofibrils were extracted from pistachio shells utilizing environmentally friendly pulping and totally chlorine-free bleaching. The extracted nanofibers were used to elaborate nanopaper, a continuous film made by gravimetric entanglement of the nanofibers and hot-pressed to enhance intramolecular bonding. The elaborated nanopapers were analyzed through their mechanical, optical, and surface properties to evaluate the influence of non-cellulosic macromolecules on the final properties of the nanopaper. Results have shown that the presence of lignin augmented the viscoelastic properties of the nanopapers by ≈25% compared with fully bleached nanopaper; moreover, the hydrophobicity of the lignocellulose nanopaper was achieved, as the surface free energy was diminished from 62.65 to 32.45 mNm−1 with an almost non-polar component and a water contact angle of 93.52°. On the other hand, the presence of lignin had an apparent visual effect on the color of the nanopapers, with a ΔE of 51.33 and a ΔL of −44.91, meaning a substantial darkening of the film. However, in terms of ultraviolet transmittance, the presence of lignin resulted in a practically nonexistent transmission in the UV spectra, with low transmittance in the visible wavelengths. In general, the presence of lignin resulted in the enhancement of selected properties which are desirable for packaging materials, which makes pistachio shell nano-lignocellulose an attractive option for this field.The authors would like to acknowledge the University of the Basque Country UPV/EHU for financially supporting this work. E.R. wishes to acknowledge the tenure track position “Biobased materials” part of E2S UPPA supported by the “Investissements d’Avenir” French program managed by ANR (ANR-16-IDEX-0002). N.I. wishes to acknowledge the Basque Government for financial support through the PIF19-183 contract

Fine-tune of lignin properties by its fractionation with a sequential organic solvent extraction

[EN] In this work, different lignins were obtained from two different extraction methods (kraft and organosolv) but from the same raw material (Eucalyptus globulus sp.). They were subsequently fractionated to determine the differences of each extraction method and their corresponding physicochemical properties found in fractionation sequence and obtained fractions. The goal of the fractionation was to obtain lignin fractions with narrower molecular weight distribution and lower polydispersity index (PI). The solvent sequence was designed based on the environmental friendly properties, health and safety assessments of the selected organic solvents: (methanol (MeOH), ethanol (EtOH), propan-2-one (DMK), ethyl acetate (EtOAc), propan-1-ol (nPrOH), propan-2-ol (iPrOH), butan-2-one (MEK), and butan-1-ol (tBuOH)). The different fractions obtained were characterised to determine their chemical structure by several analytical techniques, such as Fourier Transformed Infrared Spectroscopy (FTIR), Ultraviolet (UV), Phosphorus-31 Nuclear Magnetic Resonance (P-31 NMR), Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS), Thermogravimetric analysis (TGA), and Differential scanning calorimetry (DSC). In addition, Gel Permeation Chromatography (GPC) was used to obtain the molecular weight distribution. This study showed an effective method for obtaining homogeneous lignins with specific structures and properties depending on the solvent and molecular weight attained. Moreover, the method designed was found to be effective regardless of the lignin extraction process employed; besides, various lignin fractions were obtained which were different from each other, having specific target applications depending on their structure and chemical properties, ranging from small molecules with abundant reactive sites to act as active materials or copolymer reagents for many applications, to larger and more inactive molecules with higher thermal resistivity.The authors would like to acknowledge the Basque Government for the financial support of this research through project IT1008-16 and grant PIF19-183. Furthermore, E. R. wants to acknowledge the tenure track position "BOIS" part of E2S UPPA supported by the "Investisse-ments d'Avenir" French program managed by ANR (ANR-16-IDEX-0002)

Variants at the 9p21 locus and melanoma risk

Background: The influence of variants at the 9p21 locus on melanoma risk has been reported through investigation of CDKN2A variants through candidate gene approach as well as by genome wide association studies (GWAS). Methods: In the present study we genotyped, 25 SNPs that tag 273 variants on chromosome 9p21 in 837 melanoma cases and 1154 controls from Spain. Ten SNPs were selected based on previous associations, reported in GWAS, with either melanocytic nevi or melanoma risk or both. The other 15 SNPs were selected to fine map the CDKN2A gene region. Results: All the 10 variants selected from the GWAS showed statistically significant association with melanoma risk. Statistically significant association with melanoma risk was also observed for the carriers of the variant T-allele of rs3088440 (540 C>T) at the 3' UTR of CDKN2A gene with an OR 1.52 (95% CI 1.14-2.04). Interaction analysis between risk associated polymorphisms and previously genotyped MC1R variants, in the present study, did not show any statistically significant association. Statistical significant association was observed for the interaction between phototypes and the rs10811629 (located in intron 5 of MTAP). The strongest association was observed between the homozygous carrier of the A-allele and phototype II with an OR of 15.93 (95% CI 5.34-47.54). Conclusions: Our data confirmed the association of different variants at chromosome 9p21 with melanoma risk and we also found an association of a variant with skin phototypes

Sentinel lymph node biopsy vs. Observation in thin melanoma: A multicenter propensity score matching study

The therapeutic value of sentinel lymph node biopsy (SLNB) in thin melanoma remains controversial. The aim of this study is to determine the role of SLNB in the survival of thin melanomas (≤1 mm). A multicenter retrospective observational study was designed. A propensity score matching was performed to compare patients who underwent SLNB vs. observation. A multivariate Cox regression was used. A total of 1438 patients were matched by propensity score. There were no significant differences in melanoma-specific survival (MSS) between the SLNB and observation groups. Predictors of MSS in the multivariate model were age, tumor thickness, ulceration, and interferon treatment. Results were similar for disease-free survival and overall survival. The 5- and 10-year MSS rates for SLN-negative and -positive patients were 98.5% vs. 77.3% (p < 0.001) and 97.3% vs. 68.7% (p < 0.001), respectively. SLNB does not improve MSS in patients with thin melanoma. It also had no impact on DSF or OS. However, a considerable difference in MSS, DFS, and OS between SLN-positive and -negative patients exists, confirming its value as a prognostic procedure and therefore we recommend discussing the option of SLNB with patients

Riesgo aumentado del desarrollo de un segundo melanoma cutáneo primario sobre un nevo en pacientes diagnosticados previamente de melanoma cutáneo primario sobre nevo

Es van analitzar les característiques de 981 malalts diagnosticats de melanoma cutani, dels quals 47 havien desenvolupat un segon melanoma. L'edat inferior a 40 anys, la localització en el tronc i el subtipus histològic d'extensió superficial, van ser factors de risc independents per al desenvolupament d'un primer melanoma sobre nevo. L'únic factor que es va associar al desenvolupament d'un segon melanoma sobre nevo, va ser que el primer també haguera mostrat esta associació. Estes troballes recalquen la importància preventiva de la vigilància dels nevos en malalts amb melanoma, sobretot quan este es desenvolupa sobre un nevo.Se analizaron las características de 981 pacientes diagnosticados de melanoma cutáneo, de los cuales 47 habían desarrollado un segundo melanoma. La edad inferior a 40 años, la localización en el tronco y el subtipo histológico de extensión superficial, fueron factores de riesgo independientes para el desarrollo de un primer melanoma sobre nevo. El único factor que se asoció al desarrollo de un segundo melanoma sobre nevo, fue que el primero también hubiera mostrado esta asociación. Estos hallazgos recalcan la importancia preventiva de la vigilancia de los nevos en pacientes con melanoma, sobre todo cuando este se desarrolla sobre un nevo

Contribution of Common Genetic Variants to Familial Aggregation of Disease and Implications for Sequencing Studies

Despite genetics being accepted as the primary cause of familial aggregation for most diseases, it is still unclear whether afflicted families are likely to share a single highly penetrant rare variant, many minimally penetrant common variants, or a combination of the two types of variants. We therefore use recent estimates of SNP heritability and the liability threshold model to estimate the proportion of afflicted families likely to carry a rare, causal variant. We then show that Polygenic Risk Scores (PRS) may be useful for identifying families likely to carry such a rare variant and therefore for prioritizing families to include in sequencing studies with that aim. Specifically, we introduce a new statistic that estimates the proportion of individuals carrying causal rare variants based on the family structure, disease pattern, and PRS of genotyped individuals. Finally, we consider data from the MelaNostrum consortium and show that, despite an estimated PRS heritability of only 0.05 for melanoma, families carrying putative causal variants had a statistically significantly lower PRS, supporting the idea that PRS prioritization may be a useful future tool. However, it will be important to evaluate whether the presence of rare mendelian variants are generally associated with the proposed test statistic or lower PRS in future and larger studies