Development of a 200 single nucleotide polymorphism panel for parentage assessment for 14 Italian goat breeds

The recent availability of a medium density SNPs chip in goat offers the possibility to develop a useful and less expensive tool for parentage assessment. However, standard approaches of SNP selection for parentage assignment are still ineffective due to a lack of information about markers position. In this study, we describe the identification of a 200 SNPs panel for parentage testing in goat. Data on 350 goats of 14 different Italian breeds genotyped with the Illumina 50K SNP array were provided by the Italian Goat Consortium (IGC). The 200 SNPs panel was identified by a three-step procedure, as follows: 1) parentage assessment by mendelian errors and genomic parentage to identify true parent-offspring pairs; 2) identification of informative SNPs by canonical discriminant analysis and 3) reduction by mendelian errors and stepwise regression. The 200 SNPs panel was tested on pairwise comparison of all animals at each locus. Sensitivity, specificity and accuracy of the panel were assessed. The probability of exclusion (Pe) and the probability of a random coincidental match inclusion (Pi) for each breed were estimated. The panel showed good assessment power, with high sensitivity (0.9429), specificity (1.0) and accuracy (0.99997). Pe values ranged from a minimum of 0.99999981 for Maltese from Sardinia to a maximum of 0.999999999996 for Nicastrese. We further reduced panel size by stepwise regression to 174 SNPs showing the same performance of the 200 SNP panel. The development of tools for parentage assessment could improve breeding management also in species with low genetic information, as goat

Open data from the third observing run of LIGO, Virgo, KAGRA, and GEO

The global network of gravitational-wave observatories now includes five detectors, namely LIGO Hanford, LIGO Livingston, Virgo, KAGRA, and GEO 600. These detectors collected data during their third observing run, O3, composed of three phases: O3a starting in 2019 April and lasting six months, O3b starting in 2019 November and lasting five months, and O3GK starting in 2020 April and lasting two weeks. In this paper we describe these data and various other science products that can be freely accessed through the Gravitational Wave Open Science Center at https://gwosc.org. The main data set, consisting of the gravitational-wave strain time series that contains the astrophysical signals, is released together with supporting data useful for their analysis and documentation, tutorials, as well as analysis software packages

Parentage assessment with 200 single nucleotide polymorphisms on 15 Italian goat breeds

In this study we describe a panel of 200 SNPs for parentage testing in goat, optimized on 15 Italian breeds. Data on 350 goats genotyped with the Illumina 50K SNP array were provided by the Italian Goat Consortium (IGC). Animals belong to 15 breeds/populations farmed in North (Saanen, Alpine, Valdostana, Orobica, Bionda dell\u2019Adamello and Valpassiria), Center (Teramana and Grigia Ciociara), South Italy and Islands (Aspromontana, Nicastrese, Girgentana, Argentata dell\u2019Etna, Maltese, Maltese Sarda e Sarda). Quality editing excluded 2,211 SNPs with minor allele frequency <1%, genotype call rate <95% and individual call rate <90%. Genomic Parentage (GP) and Mendelian Errors (ME) were assessed on the 350 goats using the remaining 51,136 markers. Pairs of individuals were classified as Parent-Offspring (PO) when ME<1000 and GP 650.4. A total of 34 PO were identified out of 61,075 pairwise comparisons. We developed a novel method based on multivariate discriminant analysis and stepwise regression for choosing the best SNPs for parentage testing. Following ISAG standards for parentage testing in cattle, we identified a 200 SNP subset suitable to parentage testing in goat based on pairwise ME calculation. We considered PO all pairs of animals sharing 641 ME, doubtful all pairs sharing 2-3 ME and unrelated all pairs sharing >3 ME. The sensibility, specificity and accuracy (false negative, false positive and true assignment ratio, respectively) of the panel were assessed. In addition, we estimated the probability of single parental exclusion (Pe) and the probability of a random coincidental match inclusion (Pi) for each breed. The parentage panel showed good assessment power, with high specificity (0.9705882), sensibility (1.0) and accuracy (0.9999836). Pe values ranged from a minimum of 0.9999995 for Teramana to a maximum of 1.0 for Alpine. Pi values ranged from 8.49 X 10-78 for Alpine to 1.21 X 10-61 for Teramana. Pe for single SNP ranged from 0.0677\ub10.0592 to 0.1085\ub10.0506 (mean\ub1SD) for Teramana and Alpine, respectively. This is the first SNP panel available for parentage testing in goat. Our results suggest that genomic research can help solve practical problems in breeding, such as pedigree registration errors. In this context, cost-effective parentage testing would help goat breeders in the management of consanguinity

Supplementary Material for: The Prognosis of Nail Apparatus Melanoma: 20 Years of Experience from a Single Institute

<b><i>Introduction and Objectives:</i></b> Nail apparatus melanoma (NAM) is an uncommon tumor, especially in Caucasians. The prognosis of patients affected by NAM was analyzed and correlated with the histopathological criteria and the surgical management of the tumors. <b><i>Materials and Methods: </i></b>We collected data regarding NAM referred to the Skin Cancer Unit of the Dermatology Department of the University of Bologna, from 1992 to January 2012. <b><i>Results:</i></b> Out of 1,327 melanoma cases diagnosed between 1992 and 2012, 42 patients were affected by NAM (2.93%). All the patients were Caucasian. Two deceased patients with insufficient medical records and 1 woman with a personal history of breast cancer were excluded. Thirty-nine cases entered this study: 24 were women (67%) and 15 men (33%). The mean age at diagnosis of NAM was 57.3 years (range 29-88 years). Statistical analyses showed that prognosis was significantly correlated with the Breslow thickness (≥/<2 mm; p = 0.02), regression (p < 0.0001) and ulceration (p = 0.04). Regarding surgical management, Kaplan-Meier's test pointed out that performing functional surgery compared to disarticulation did not correlate with a better prognosis of patients (p = 0.08). <b><i>Conclusions:</i></b> In our experience, the surgical management (disarticulation with respect to functional surgical excision) did not influence the prognosis of NAM patients. The latter was affected by the histopathological characteristics (Breslow thickness, regression and mitoses) and location (fingers vs. foot)

Association between Clinical Frailty Scale score and hospital mortality in adult patients with COVID-19 (COMET): an international, multicentre, retrospective, observational cohort study

Background: During the COVID-19 pandemic, the scarcity of resources has necessitated triage of critical care for patients with the disease. In patients aged 65 years and older, triage decisions are regularly based on degree of frailty measured by the Clinical Frailty Scale (CFS). However, the CFS could also be useful in patients younger than 65 years. We aimed to examine the association between CFS score and hospital mortality and between CFS score and admission to intensive care in adult patients of all ages with COVID-19 across Europe. Methods: This analysis was part of the COVID Medication (COMET) study, an international, multicentre, retrospective observational cohort study in 63 hospitals in 11 countries in Europe. Eligible patients were aged 18 years and older, had been admitted to hospital, and either tested positive by PCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or were judged to have a high clinical likelihood of having SARS-CoV-2 infection by the local COVID-19 expert team. CFS was used to assess level of frailty: fit (CFS1–3), mildly frail (CFS4–5), or frail (CFS6–9). The primary outcome was hospital mortality. The secondary outcome was admission to intensive care. Data were analysed using a multivariable binary logistic regression model adjusted for covariates (age, sex, number of drugs prescribed, and type of drug class as a proxy for comorbidities). Findings: Between March 30 and July 15, 2020, 2434 patients (median age 68 years [IQR 55–77]; 1480 [61%] men, 954 [30%] women) had CFS scores available and were included in the analyses. In the total sample and in patients aged 65 years and older, frail patients and mildly frail patients had a significantly higher risk of hospital mortality than fit patients (total sample: CFS6–9 vs CFS1–3 odds ratio [OR] 2·71 [95% CI 2·04–3·60], p<0·0001 and CFS4–5 vs CFS1–3 OR 1·54 [1·16–2·06], p=0·0030; age ≥65 years: CFS6–9 vs CFS1–3 OR 2·90 [2·12–3·97], p<0·0001 and CFS4–5 vs CFS1–3 OR 1·64 [1·20–2·25], p=0·0020). In patients younger than 65 years, an increased hospital mortality risk was only observed in frail patients (CFS6–9 vs CFS1–3 OR 2·22 [1·08–4·57], p=0·030; CFS4–5 vs CFS1–3 OR 1·08 [0·48–2·39], p=0·86). Frail patients had a higher incidence of admission to intensive care than fit patients (CFS6–9 vs CFS1–3 OR 1·54 [1·21–1·97], p=0·0010), whereas mildly frail patients had a lower incidence than fit patients (CFS4–5 vs CFS1–3 OR 0·71 [0·55–0·92], p=0·0090). Among patients younger than 65 years, frail patients had an increased incidence of admission to intensive care (CFS6–9 vs CFS1–3 OR 2·96 [1·98–4·43], p<0·0001), whereas mildly frail patients had no significant difference in incidence compared with fit patients (CFS4–5 vs CFS1–3 OR 0·93 [0·63–1·38], p=0·72). Among patients aged 65 years and older, frail patients had no significant difference in the incidence of admission to intensive care compared with fit patients (CFS6–9 vs CFS1–3 OR 1·27 [0·92–1·75], p=0·14), whereas mildly frail patients had a lower incidence than fit patients (CFS4–5 vs CFS1–3 OR 0·66 [0·47–0·93], p=0·018). Interpretation: The results of this study suggest that CFS score is a suitable risk marker for hospital mortality in adult patients with COVID-19. However, treatment decisions based on the CFS in patients younger than 65 years should be made with caution. Funding: LOEY Foundation