Effects of marker density and minor allele frequency on genomic prediction for growth traits in Chinese Simmental beef cattle

Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding. However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding values （GEBVs）. To investigate the impact of marker density and minor allele frequency on predictive ability, we estimated GEBVs by constructing the different subsets of single nucleotide polymorphisms （SNPs） based on varying markers densities and minor allele frequency （MAF） for average daily gain （ADG）, live weight （LW） and carcass weight （CW） in 1 059 Chinese Simmental beef cattle. Two strategies were proposed for SNP selection to construct different marker densities： 1） select evenly-spaced SNPs （Strategy 1 ）, and 2） select SNPs with large effects estimated from BayesB （Strategy 2）. Furthermore, predictive ability was assessed in terms of the correlation between predicted genomic values and corrected phenotypes from 10-fold cross-validation. Predictive ability for ADG, LW and CW using autosomal SNPs were 0.13＋0.002, 0.21＋0.003 and 0.25＋0.003, respectively. In our study, the predictive ability increased dramatically as more SNPs were included in analysis until 200K for Strategy 1. Under Strategy 2, we found the predictive ability slightly increased when marker densities increased from 5K to 20K, which indicated the predictive ability of 20K （3% of 770K） SNPs with large effects was equal to the predictive ability of using all SNPs. For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01-0.1. Our result suggested that designing a low-density chip by selecting low frequency markers with large SNP effects sizes should be helpful for commercial application in Chinese Simmental cattle.

Envita’s Precision Cancer Care: 35-Fold Improvement in Response Rates

New clinical approaches are imperative beyond the widely adopted National Comprehensive Cancer Network (NCCN) guidelines, utilized by prominent cancer institutions. Cancer is the leading cause of death among individuals younger than 85 years within the United States. Despite significant technological advances, including the expenditure of hundreds of billions, treatment outcomes and overall survival have not notably improved for most types of advanced cancer over the last several decades. Over the past 24 years, Envita Medical Centers has pioneered a unique form of personalized treatment approach for late-stage and refractory cancer patients, introducing groundbreaking innovations in the field. Our integrated algorithm utilizes advanced genomics, transcriptomics, and highly tailored immunotherapy, resulting in remarkable outcome improvements. This study presents Envita’s innovative personalized treatment algorithms and examines the response outcomes of 199 late-stage cancer patients treated at Envita Medical Centers over a two-year period. Compared to standard of care and palliative chemotherapy, Envita’s treatment demonstrated a remarkable 35-fold improvement in overall response rates (Figure 1). Moreover, 88% of the patients, the majority presenting with Stage 3 or 4 cancer, experienced a 43-fold improvement in quality of life with minimal side effects, as compared to standard of care chemotherapy and palliative care. This revolutionary success is attributed to Envita’s personalized therapeutic algorithms, which incorporate customized immunotherapy. Envita’s precision care approach has also achieved a 100% better response rate compared to over 65 global chemotherapy clinical trials with more than 2700 patients. The results from this study suggest that a wider utilization of Envita’s personalized approach can significantly benefit patients with late-stage and refractory cancer.

A Positive Correlation between Elevated Altitude and Frequency of Mutant Alleles at the EPAS1 and HBB Loci in Chinese Indigenous Dogs

Hypoxia represents one of the most extreme environmental conditions for both human beings and animals living at high al- titudes （Zhao et al., 2009）. Over the past few years, great attention has been focused on the genetic bases of adaption to high-altitude environments （Bigham et al., 2010; Simonson et al., 2010）. The domestic dog （Canisfamiliaris） is the first animal that developed an intimate relationship with human beings. Dogs migrated with human beings and have adapted to variety of ecological niches （Savolainen et al., 2002）. Our previous research revealed parallel evolution and convergent evolution in the adaptation of dogs and humans to the high-altitude environment of the Tibetan plateau （Wang et al., 2013, 2014）, suggesting that exploring the adaption of domestic dogs to high-altitude hypoxia is an interesting and important question.

云南省景颇族人群HIV-1感染相关基因多态性研究

目的:了解云南省景颇族人群与HIV-1感染相关基因CCR5-Δ32、CCR2-64I、SDF1-3′A的频率和多态性分布。方法:以云南省113例景颇族人群为研究对象,采用PCR、PCB/RFLP(聚合酶链式反应/限制性片段长度多态性分析)计算基因频率,并用统计学方法进行分析。结果:未发现CCR5-Δ32突变;CCR2-64I突变基因频率为16.37％;SDF1-3′G/3′G突变基因频率为17.70％,突变基因频率低于汉族。结论:由于未发现CCR5-Δ32突变和SDF1-3′G/3′G等位基因频率较低,云南省景颇族人群可能比汉族人对HIV-1(包括R5和X4HIV-1)有较大的遗传易感性。

闽东地区畲族人群CYP2C19基因多态性分析

目的:调查闽东地区汉族与畲族人群CYP2C19基因多态性分布情况。方法:采用限制性片段长度多态性聚合酶链反应(PCR-RFLP),对汉族(n=140)与畲族(n=180)人群CYP2C19两个多态性位点CYP2C19*2和CYP2C19*3的基因多态性进行分析,用SPSS16.0软件进行统计分析,Hardy-Weinberg遗传平衡定律验证基因型分布情况。结果:汉族与畲族人群各种基因型出现频率分别为:*1/*1 14.3%,28.9%;*1/*2 28.6%,30.0%;*1/*3 11.4%,16.7%;*2/*2 21.4%,9.4%;*2/*3 21.4%,12.8%;*3/*3 2.9%,2.2%。汉族与畲族CYP2C19不同等位基因出现频率:*1为34.3%,52.2%;*2为46.4%,30.8%;*3为19.3%,16.9%。结论:闽东地区畲族与汉族CYP2C19*2与*3等位基因突变率存在差异,畲族人群基因突变率低于汉族(P<0.05)。