Mulugeta, T. | Search bioRxiv

bioRxiv2020

The structural variation landscape in 492 Atlantic salmon genomes

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

genomics↗

bioRxiv2019

Survival status and predictors of mortality among Breast cancer patients at Black lion specialized hospital, Adult oncology unit, Addis Ababa, Ethiopia, 2018. A retrospective follow-up study with survival analysis

IntroductionBreast cancer is a foremost cause of death worldwide, ranks fifth among causes of death from all types of cancers; this is the most common cause of cancer death in women among both developing and developed countries. Breast cancer ranks first among most frequent cancers in women of Ethiopia. In spite of the high incidence, mortality rate, and survival status among breast cancer patients was not determined in Ethiopia.\n\nObjectiveThe main aim of the study is to assess the survival status and predictor the mortality among Breast Cancer patients in Adult Oncology Unit at Black Lion Specialized Hospital in 2018.\n\nMethodsAn institution based retrospective follow up study was conducted in Adult Oncology Unit at Black Lion Specialized Hospital. All cases of breast cancer registered from 1st January 2012 to 31th December,2014 were followed for the six-year survival (until 31th December, 2017). Kaplan-Meier survival curve together with log rank test was deployed to test for variations in the survival among predictor variables. Cox regression was used at 5% level of significance to determine the net effect of each independent variable on time to death of breast cancer clients.\n\nResultsThe results indicate that the incidence rate of mortality was 9.8 per 100 person/ years (95% CI: 8.49-11.47).The overall median survival time was 56.5(95% CI (53.46 - 60.83)) months. The overall estimated survival rate was recorded 27% (95% CI, 17.09 to 36.67 %) at 72 months of follow up, whereas at odd years (1, 3, and 5 years) were, 97.2%, 80.8%, and 46.2% respectively. Predictors of mortality were assessed at clinical stage (III&IV),(AHR =1.86), poorly differentiated histology (AHR: 3.1) & positive lymph node status (AHR:3.13),Whereas adjuvant hormone therapy (AHR: 0.67) and chemotherapy (AHR:0.72) were protective.\n\nConclusionThe overall probability of survival in Ethiopia was inferior when compared with other high and middle-income countries. Predictors of mortality were at advanced clinical stage, poorly differentiated histology grade, surgical margin involvement and positive lymph node status. In contrary, adjuvant hormone therapy, modified radical mastectomy and chemotherapy were protective factors. Hence, special emphasis could be given to early screening, stage diagnosis and initiation of treatment.

epidemiology↗