Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

peer-reviewedRuns of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation.Cino Pertoldi was supported by a grant from Danish Natural Science Research Council (Grant nos. 11-103926, 09-065999, and 95095995), the Carlsberg Foundation (Grant no. 2011- 01-0059), and the Aalborg Zoo Conservation Foundation (AZCF). Laura Iacolina has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Action (Grant Agreement no. 656697). Astrid V. Stronen received funding from the Danish Natural Science Research Council (Postdoctoral Grant 1337-00007)

Fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin with gemtuzumab ozogamicin improves event-free survival in younger patients with newly diagnosed aml and overall survival in patients with npm1 and flt3 mutations

Purpose To determine the optimal induction chemotherapy regimen for younger adults with newly diagnosed AML without known adverse risk cytogenetics. Patients and Methods One thousand thirty-three patients were randomly assigned to intensified (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin [FLAG-Ida]) or standard (daunorubicin and Ara-C [DA]) induction chemotherapy, with one or two doses of gemtuzumab ozogamicin (GO). The primary end point was overall survival (OS). Results There was no difference in remission rate after two courses between FLAG-Ida + GO and DA + GO (complete remission [CR] + CR with incomplete hematologic recovery 93% v 91%) or in day 60 mortality (4.3% v 4.6%). There was no difference in OS (66% v 63%; P = .41); however, the risk of relapse was lower with FLAG-Ida + GO (24% v 41%; P < .001) and 3-year event-free survival was higher (57% v 45%; P < .001). In patients with an NPM1 mutation (30%), 3-year OS was significantly higher with FLAG-Ida + GO (82% v 64%; P = .005). NPM1 measurable residual disease (MRD) clearance was also greater, with 88% versus 77% becoming MRD-negative in peripheral blood after cycle 2 (P = .02). Three-year OS was also higher in patients with a FLT3 mutation (64% v 54%; P = .047). Fewer transplants were performed in patients receiving FLAG-Ida + GO (238 v 278; P = .02). There was no difference in outcome according to the number of GO doses, although NPM1 MRD clearance was higher with two doses in the DA arm. Patients with core binding factor AML treated with DA and one dose of GO had a 3-year OS of 96% with no survival benefit from FLAG-Ida + GO. Conclusion Overall, FLAG-Ida + GO significantly reduced relapse without improving OS. However, exploratory analyses show that patients with NPM1 and FLT3 mutations had substantial improvements in OS. By contrast, in patients with core binding factor AML, outcomes were excellent with DA + GO with no FLAG-Ida benefit

Quality of life and complications after nephron-sparing treatment of renal cell carcinoma stage T1-a systematic review

BACKGROUND: Despite the fact that nephron-sparing treatment is considered preferable from a surgical perspective patients’ quality of life (QoL) following different types of nephron-sparing treatments remains unclear. PURPOSE: To investigate the quality of life and complications after nephron-sparing treatment of renal cell carcinomas of stage T1. MATERIALS AND METHODS: A systematic search of six databases was carried out. We included studies that reported the quality of life and complications in patients aged 18 years or older following nephron-sparing treatment of renal cell carcinoma stage T1. The quality assessment was performed using the Critical Appraisal Skills Programme (CASP) checklist for cohort studies and the CASP Randomized Controlled Trial Checklist. Data were analyzed using a narrative approach. RESULTS: Eight studies were included, six of which investigated QoL after partial nephrectomy and two after ablation therapies. Seven studies reported complications. Three studies reported higher QoL scores after partial nephrectomy compared to radical nephrectomy. Two studies showed that QoL increased or returned to baseline levels up to 12 months following partial nephrectomy. One study reported a gradual increase in QoL after radiofrequency ablation, and one study reported that all patients recovered to baseline QoL following cryoablation. Across studies, we found a complication rate up to 20% after partial nephrectomy and up to 12.5% after ablation therapy. CONCLUSIONS: The results of this systematic review suggest that nephron-sparing treatment appears to be superior or comparable to other treatment alternatives with regard to QoL outcomes. Additionally, based on the studies included in this review, partial nephrectomy appears to have a higher complication rate compared with ablation therapies. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42020155594 SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13643-021-01868-2