EAT and AAI, along eigenvector 1, which explains ~15% of the total variation. AFT Muturu and N'Dama are close to EAT along the eigenvector 1. Most of the AFH cattle cluster together regardless of their breed memberships, leaving only Ankole, Mursi and Sheko outside the main cluster toward the AFT Muturu and N'Dama. The PCA results also show that Muturu and N'Dama, our representative of AFT population, are separated from the other cattle groups (eigenvector 2, ~2.5% of total variation). Sheko positions close to the AFH, as similarly reported in other studies 5,43 . Genetic clustering analysis using ADMIXTURE 44 corroborates the pattern found in PCA (Fig. 2b and Extended Data Fig. 2). Most of AFH show a similar proportion of taurine ancestry, around 25% on average. Only a few AFH breeds have elevated taurine ancestry: Ankole (53.37 ± 1.49%), Sheko (46.28 ± 2.03%) and Mursi (35.90 ± 2.16%). (Fig. 2b).Genetic distance and diversity. Pairwise F st were calculated to estimate the genetic distances between populations (n = 38) (Extended Data Fig. 3). Taurine (EUT, AST and AFT) show F st values of 0.1568 and 0.3287 on average against AFH and AAI, respectively.Across AFH, pairwise F st between breeds is close to zero, regardless of their phenotypic classification as African Zebu, Sanga or Zenga. Muturu and N'Dama show F st value of 0.1769, 0.1847 and 0.3734 against AFH, EAT and AAI, respectively.The genome-wide autosomal SNPs show reduced levels of heterozygosity in the taurine (0.0021 ± 0.0005/bp) compared to all other populations (0.0048 ± 0.0008/bp). Heterozygosity values of AFH are similarly higher across populations (0.0046 ± 0.0003/bp). AAI shows a higher level of heterozygosity compared to AFH (0.0052 ± 0.0014/bp) (Extended Data Fig. 4). The degree of inbreeding measured by runs of homozygosity (ROH) shows that taurine, including Muturu and N'Dama, have a higher level of inbreeding compared to the other and Ethiopia), the University of Khartoum (Sudan), and the National Biotechnology Development Agency (NABDA) (Nigeria). The following institutions and their personnel provided help for the sampling of the African cattle: ILRI Kapiti Ranch, Ministry of Animal Resources, Fisheries and Range (Sudan), Ol Pejeta Conservancy (Kenya), Institute of Biodiversity (Ethiopia), the Directors of Veterinary Services and the cattle keepers from Ethiopia, Kenya, Uganda and Sudan. ILRI livestock genomics program is supported by the

Highly sensitive genotyping assays can detect mutations in cell-free DNA (cfDNA) from cancer patients, reflecting the biology of each patient’s cancer. Because circulating tumor DNA comprises a small, variable fraction of DNA circulating in the blood, sensitive parallel multiplexing tests are required to determine mutation profiles. We prospectively examined the clinical utility of ultra-deep sequencing analysis of cfDNA from 126 non-small cell lung cancer (NSCLC) patients using the Ion AmpliSeq Cancer Hotspot Panel v2 (ICP) and validated these findings with droplet digital polymerase chain reaction (ddPCR). ICP results were compared with tumor tissue genotyping (TTG) results and clinical outcomes. A total of 853 variants were detected, with a median of four variants per patient. Overall concordance of ICP and TTG analyses was 90% for EGFR exon 19 deletion and 88% for the L858R mutation. Of 34 patients with a well-defined EGFR activating mutation defined based on the results of ICP and TTG, 31 (81.6%) showed long-term disease control with EGFR TKI treatment. Of 56 patients treated with an EGFR tyrosine kinase inhibitor (TKI), the presence of the de novo T790M mutation was confirmed in 28 (50%). Presence of this de novo mutation did not have a negative effect on EGFR TKI treatment. Ultra-deep sequencing analysis of cfDNA using ICP combined with confirmatory ddPCR was effective at defining driver genetic changes in NSCLC patients. Comprehensive analysis of tumor DNA and cfDNA can increase the specificity of molecular diagnosis, which could translate into tailored treatment.

Background & Aims: The application of circulating tumor DNA (ctDNA) has been studied for predicting recurrent disease after surgery and treatment response during systemic treatment. Metastasectomy can be curative for well-selected patients with metastatic colorectal cancer (mCRC). This prospective study investigated the ctDNA level before and after metastasectomy in patients with mCRC to explore its potential as a predictive biomarker. Methods: We collected data on 98 metastasectomies for mCRC performed from March 2017 to February 2020. Somatic mutations in the primary and metastatic tumors were identified and tumor-informed ctDNAs were selected by ultra-deep targeted sequencing. Plasma samples were mandatorily collected before and 3–4 weeks after metastasectomy and serially, if patients agreed. Results: Data on 67 of 98 metastasectomies (58 patients) meeting the criteria were collected. ctDNA was detected in 9 (29%) of 31 cases treated with upfront metastasectomy and in 7 (19.4%) of 36 cases treated with metastasectomy after upfront chemotherapy. The detection rate of ctDNA was higher in liver metastasis (p = 0.0045) and tumors measuring ≥1 cm (p = 0.0183). ctDNA was less likely to be detected if the response to chemotherapy was good. After metastasectomy, ctDNA was found in 4 (6%) cases with rapid progressive disease. Conclusion: The biological factors affecting the ctDNA shedding from the tumor should be considered when applying ctDNA assays in a clinical setting. After metastasectomy for oligometastatic lesions in good responders of chemotherapy, most ctDNA was cleared or existed below the detection level. To assist clinical decision making after metastasectomy for mCRC using ctDNA, further studies for improving specific outcomes are needed.

Cigarette smoke (CS) affects the expression of microRNAs (miRNAs), which are important regulators of gene expression by inducing DNA methylation. However, the effects of smoking on miRNA expression have not been fully elucidated in smoking-related lung carcinogenesis. Therefore, in this study, to investigate the change of miRNA expression pattern and to identify tumor suppressor miRNAs by smoking in lung carcinogenesis, we used lung carcinogenesis model cell lines that, derived from a murine xenograft model with human bronchial epithelial cells (BEAS-2B), exposed CS or not. The microarray analysis revealed that miR-584-5p expression was downregulated with cancer progression in lung carcinogenesis model cell lines. We confirmed by pyrosequencing that the methylation level of the miR-584-5p promoter increased with cancer progression. In vitro and in vivo experiments showed that miR-584-5p suppressed migration and invasion in non-small cell lung cancer (NSCLC) cells by targeting YKT6. Furthermore, we showed that high level of YKT6 was associated with a poor survival rate in NSCLC patients with a history of smoking. These results suggest that miR-584-5p acts as a tumor suppressor and is a potential molecular biomarker for smoking-related NSCLC.

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