METHOD: The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization.
RESULTS: Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach.
CONCLUSION: We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.
METHODS: Total numbers and age-standardized rates per 100,000 population for MASLD prevalence, annual incidence, and YLDs were compared across regions and countries by age, sex, and sociodemographic index (SDI). Smoothing spline models were used to evaluate the relationship between the burden of MASLD and SDI. Estimates were reported with uncertainty intervals (UI).
RESULTS: Globally, in 2021, the age-standardized rates per 100,000 population of point prevalence of MASLD were 15,018.1 cases (95% UI 13,756.5-16,361.4), annual incidence rates were 608.5 cases (598.8-617.7), and YLDs were 0.5 (0.3-0.8) years. MASLD point prevalence was higher in men than women (15,731.4 vs. 14,310.6 cases per 100,000 population). Prevalence peaked at ages 45-49 for men and 50-54 for women. Kuwait (32,312.2 cases per 100,000 people; 95% UI: 29,947.1-34,839.0), Egypt (31,668.8 cases per 100,000 people; 95% UI: 29,272.5-34,224.7), and Qatar (31,327.5 cases per 100,000 people; 95% UI: 29,078.5-33,790.9) had the highest prevalence rates in 2021. The largest increases in age-standardized point prevalence estimates from 2010 to 2021 were in China (16.9%, 95% UI 14.7%-18.9%), Sudan (13.3%, 95% UI 9.8%-16.7%) and India (13.2%, 95% UI 12.0%-14.4%). MASLD incidence varied with SDI, peaking at moderate SDI levels.
CONCLUSIONS: MASLD is a global health concern, with the highest prevalence reported in Kuwait, Egypt, and Qatar. Raising awareness about risk factors and prevention is essential in every country, especially in China, Sudan and India, where disease incidence and prevalence are rapidly increasing.
IMPACT AND IMPLICATIONS: This research provides a comprehensive analysis of the global burden of MASLD, highlighting its rising prevalence and incidence, particularly in countries with varying sociodemographic indices. The findings are significant for both clinicians and policymakers, as they offer critical insights into the regional disparities in MASLD burden, which can inform targeted prevention and intervention strategies. However, the study's reliance on modeling and available data suggests cautious interpretation, and further research is needed to validate these findings in clinical and real-world settings.