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Revolutionizing newborn care: Machine learning and whole-genome sequencing for early diagnosis of sick newborns

Researchers have developed a method called “Mendelian Phenotype Search Engine” (MPSE) to identify which sick infants in the neonatal intensive care unit (NICU) would benefit most from newborn whole-genome sequencing. MPSE accurately identifies critically ill infants who would benefit from sequencing, improving diagnostic yields and saving valuable time for doctors and patients. Future developments in machine learning could make MPSE an even more valuable tool. Read more about this study under Article 1.

Article 1: Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning

Researchers have developed a new method to help doctors quickly identify which sick infants in the neonatal intensive care unit (NICU) would benefit most from newborn whole-genome sequencing (WGS) or rapid WGS (rWGS). The method is called the “Mendelian Phenotype Search Engine” (MPSE) and uses electronic health records to identify infants who may have undiagnosed genetic conditions that could be detected through WGS or rWGS. The MPSE accurately identified critically ill infants who would benefit from sequencing, and the researchers suggest that this automated process could be used alongside manual clinical reviews to improve diagnostic yields. Further developments in machine learning could improve the accuracy of the method even further. Read the full article here.

In summary: New method to quickly identify which sick infants benefit most from WGS

Article 2: The expression level of Neuronal Calcium Sensor 1 can predict the prognosis of cytogenetically normal AML 

Researchers have identified a potential biomarker for cytogenetically normal forms of acute myeloid leukemia (AML). The team looked at the NCS1 gene expression levels in over 500 cytogenetically normal AML cases and found that higher-than-usual levels of the gene were linked to better event-free survival and overall survival times in contrast to other cancer types where enhanced expression of the gene corresponds to poorer survival outcomes. The study suggests that NCS1 expression has great prognostic value for AML patients and can predict a favorable prognosis for those with cytogenetically normal AML. Read the full article here.

In summary: Potential biomarker for better prognosis of acute myeloid leukemia without chromosomal abnormalities discovered

Article 3: A practical checklist for return of results from genomic research in the European context

A team of experts has proposed a checklist to help researchers return genomic research results to study participants. Although returning individual genomic research results is becoming more common, there are currently no standardized guidelines. The checklist covers areas such as developing a result return plan, confirming results, and following up with participants, providing a clear outline for researchers to develop ethical and sustainable result return pathways in their projects. However, further legal analysis is necessary to ensure compliance with domestic laws. Read the full article here.

In summary: Proposed checklist for returning genomic research results to study participants

Article 4: Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients

Researchers have examined the factors that contribute to bladder cancer risk in individuals who have received solid organ transplants and are taking immunosuppressive drugs. The team analyzed tumor samples from transplant recipients who later developed bladder cancer, using whole-genome sequencing and RNA sequencing to identify genetic mutations and viral sequences that may be linked to cancer development. The researchers discovered several recurrent mutations and viral sequences, including the BK polyomavirus, in the tumor samples. They suggest that the development of bladder cancer in transplant recipients may involve unique mutagenic processes and multiple mechanisms of carcinogenesis, which could have important implications for cancer prevention, treatment, and outcomes. Read the full article here.

In summary: Factors contributing to bladder cancer risk in organ transplant recipients discovered

New in Genetics issue March 2023. Every month, Medicover Genetics curates the most important peer-reviewed scientific publications related to genetics.

References

[1] Peterson, Bennet et al. “Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning.” Genome medicine vol. 15,1 18. 16 Mar. 2023, doi:10.1186/s13073-023-01166-7 https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01166-7

[2] Zhang, Weilong et al. “The expression level of Neuronal Calcium Sensor 1 can predict the prognosis of cytogenetically normal AML.” The pharmacogenomics journal, 10.1038/s41397-023-00301-2. 14 Mar. 2023, doi:10.1038/s41397-023-00301-2 https://www.nature.com/articles/s41397-023-00301-2

[3] Vears, Danya F et al. “A practical checklist for return of results from genomic research in the European context.” European journal of human genetics: EJHG, 10.1038/s41431-023-01328-6. 22 Mar. 2023, doi:10.1038/s41431-023-01328-6 https://www.nature.com/articles/s41431-023-01328-6

[4] Starrett, Gabriel J et al. “Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients” eLife 12:e82690. https://doi.org/10.7554/eLife.82690 https://elifesciences.org/articles/82690

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