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.

Allele Frequency Distribution of the NCAPG c.1326T>G SNP Associated with Growth-Related Traits in Niigata Population of Japanese Black Beef Cattle

Growth performance as well as marbling is the main breeding objectives in Japanese Black cattle, the major beef breed in Japan. A previous study has identified the c.1326T>G single nucleotide polymorphism (SNP) in the NCAPG (non-SMC condensin I complex, subunit G) gene that leads to the amino acid change p.Ile442Met in the NCAPG protein, which is a candidate causative variation for a bovine carcass weight (CWT) quantitative trait locus (QTL). In this study, we first confirmed the association of the c.1326T>G SNP with the growth-related traits, CWT, rib eye area (REA) and rib thickness (RT), and showed significant effect of the SNP genotypes on the marbling trait, beef marbling score (BMS), in the Japanese Black beef cattle population of the Niigata prefecture, with the G allele being associated with a favorable phenotype of these traits. Thus, we concluded that the c.1326T>G SNP is useful for effective marker-assisted selection to increase meat quality and meat productivity in Japanese Black beef cattle of the Niigata prefecture. Furthermore the frequency of the favorable G allele of the c.1326T>G SNP in the Niigata prefecture population was significantly lower than the frequency of this allele in Japanese Black cattle population of the Kagoshima prefecture. However, no statistically significant difference was detected between the allele frequencies estimated by maternal alleles in the half-sib progeny steers in the Niigata prefecture population and obtained in Japanese Black cattle population of the Kagoshima prefecture.

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.

Low Frequencies of CCR5-Δ32 and CCR5-m303,but High Frequencies of CCR2-641 and SDF1-3'A Alleles in Indigenous Ethnic Groups in China's Mainland

Objective: The aim in this study was to identify the allelicfrequencies of the chemokine (SDF1-3'A) and chemokinereceptor (CCR5△32, CCR5m303 and CCR2-64I) genesresistant to HIV-1 infection and/or disease progression inindigenous Chinese populations. Methods: By using QIAamp DNA Blood Mini Kit, thegenomic DNA samples were purified from whole peripheralblood of healthy individuals (n=2067) from Han, Uygur,Mongolian and Tibetan ethnic groups, as well as Han patientsincluding HIV-1 carriers (n=330), patients with other sexuallytransmitted diseases (STDs, n=259) and intravenous drugusers (IVDUs, n=125). The allelic polymorphisms wereidentified by means of PCR or PCR-RFLP analyses. Thesequences of randomly selected amplified PCR products werefurther confirmed by direct DNA sequencing. Results: The mutant frequencies were identified to be0%～3.48% for CCR5△32, 0% for CCR5m303,19.15%～28.79% for CCR2-64 and 19.10%～28.73% for SDF1-3'A alleles, respectively, in Chinese healthy individuals fromfour ethnic groups. Our findings indicated the allelicfrequencies vary among the different ethnic groups.Furthermore, the HIV-1 carriers, STD cases and IVDUs (all ofHan ethnicity) were found to have the allelic frequencies of0%～0.19% (CCR5△32), 0% (CCR5m303), 19.31%～20.45%(CCR2-64) and 25.61%～26.83% (SDF1-3'A) with minorvariations in their frequencies between the patients andhealthy Han groups. There was no CCR5-m303 mutationfound in any subject in this study. Conclusion: The examined subjects of four Chinese ethnicorigins showed lower frequencies of CCR5△32 andCCR5m303 alleles, but higher frequencies of mutant CCR2-64I and SDF1-3'A alleles compared to those identified innorthern-European and American Caucasians. Thesignificance of the different frequencies and polymorphisms ofthe above alleles in Chinese populations needs to be furtherexamined in HIV-1/AIDS diseases.

Estimated Genetic Variance Explained by Single Nucleotide Polymorphisms of Different Minor Allele Frequencies for Carcass Traits in Japanese Black Cattle

Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.

Potential unreliability of ALK variant allele frequency in the efficacy prediction of targeted therapy in NSCLC

Anaplastic lymphoma kinase(ALK)is the most common fusion gene involved in non-small cell lung cancer(NSCLC),and remarkable response has been achieved with the use of ALK tyrosine kinase inhibitors(ALK-TKIs).However,the clinical efficacy is highly variable.Pre-existing intratumoral heterogeneity(ITH)has been proven to contribute to the poor treatment response and the resistance to targeted therapies.In this work,we investigated whether the variant allele frequencies(VAFs)of ALK fusions can help assess ITH and predict targeted therapy efficacy.Through the application of next-generation sequencing(NGS),7.2%(326/4548)of patients were detected to be ALK positive.On the basis of the adjusted VAF(adjVAF,VAF normalization for tumor purity)of four different threshold values(adjVAF<50%,40%,30%,or 20%),the association of ALK subclonality with crizotinib efficacy was assessed.Nonetheless,no statistical association was observed between median progression-free survival(PFS)and ALK subclonality assessed by adjVAF,and a poor correlation of adjVAF with PFS was found among the 85 patients who received first-line crizotinib.Results suggest that the ALK VAF determined by hybrid capture-based NGS is probably unreliable for ITH assessment and targeted therapy efficacy prediction in NSCLC.

Glutamate decarboxylase 1 gene polymorphisms are associated with respiratory symptoms in panic disorder

BACKGROUND Genetic factors play an important role in the pathogenesis of panic disorder(PD).However,the effect of genetic variants on PD remains controversial.AIM To evaluate the associations between glutamate decarboxylase 1(GAD1)gene polymorphisms and PD risk and assess the effect of GAD1 gene polymorphisms on the severity of clinical symptoms in PD.METHODS We recruited 230 PD patients and 224 healthy controls in this study.All participants were assessed for anxiety and panic symptom severity using the Hamilton Anxiety Rating Scale(HAM-A)and Panic Disorder Severity Scale(PDSS).GAD1 gene polymorphisms(rs1978340 and rs3749034)were genotyped and assessed for allele frequencies.RESULTS There were no significant differences between cases and controls in the genotype distributions or allele frequencies of GAD1(rs1978340 and rs3749034).In addition,the effect of GAD1(rs1978340 and rs3749034)on PD severity was not significant.However,regarding respiratory symptoms,patients with the GAD1 rs1978340 A/A genotype had significantly higher scores than those with the A/G or G/G genotype.CONCLUSION Here,we showed that the A/A genotype of GAD1 rs1978340 was associated with increased severity of respiratory symptoms in patients with PD.

Influence of Allele Frequency on Predicting Animal Phenotype Using Back-Propagation Artificial Neural Networks

To overcome the obstacle of the fascinating relation in predicting animal phenotype value, we have developed a neural network model to detect the complex non-linear relationships between the genotypes and phenotypes and the possible interactions that cannot be expressed with equations. In this paper, back-propagation neural network is used to discuss the influences of different allele frequencies on estimating the polygenic phenotype value. To ensure the precision of prediction, normalization was needed to train the prediction model. The results show that back-propagation artificial neural networks can be used to predict the phenotype value and perform very well in allele frequency from 0.2 to 0.8, when the allele frequency is very small （less than 0.2） or big （more than 0.8）; however, the prediction model was not reliable and the predicted value should be carefully tested.

Polymorphism of HIV-1 Resistance Genes in Dai and Jingpo Minorities of Yunnan Province

Objective To investigate the mutant frequency and polymorphism of HIV-1 resistanceCCR5-Δ32, CCR2-64I, SDF1-3’A alleles in Jingpo and Dai nationalities of YunnanMethods The study population included 101 Dai and 113 Jingpo ethnical subjects.The genotypes were respectively detected by polymerase chain reaction (PCR) or byPCR/RFLP (restriction fragment length polymorphism) assay. Mutant frequencies werecalculated and allelic polymorphism of the three genes in population was analyzed byU test.Results We didn’t find CCR5-Δ32 mutant in either Dai or Jingpo nationality. In Daiminority, the allele frequency of CCR2-64I was 21.00% and that of SDF1-3’Awas 20.30%. In Jingpo minority, the allele frequency of CCR2-64I was 16.37% and thatof SDF1-3’A was 17.70%.Conclusion Dai and Jingpo nationality of Yunnan might have a high genetic suscep-tibility to HIV-1 (including R5 and X4 HIV strains) since we didn’t find CCR5-Δ32 andthe frequency of SDF1-3’A was much lower than that of Han nationality as wasreported in other research papers.

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.

Chromosome Mapping, Expression and Polymorphism Analysis of CRABP1 Gene in Pigs

Cellular retinoic acid-binding protein 1 （CRABP1） is a well-conserved member of cytosolic lipid-binding protein family. It is an important modulator of retinoic acid signaling. Long serial analysis of gene expression （LongSAGE） analysis suggested that CRABP1 gene was differentially expressed during prenatal skeletal muscle development in porcine. Here, we obtained the full-length coding region sequence and genomic sequence of the porcine CRABP1 gene and analyzed its genomic structures. Subsequently, we examined CRABP1 chromosome assignment using INRA-University of Minnesota 7 000 porcine radiation hybrid panel （IMpRH） and explored its tissue distribution in adult Tongcheng pigs and dynamical expression profiles in prenatal skeletal muscle （33, 65 and 90 days post coitus, dpc） from Landrace （lean-type） （described as L33, L65 and L90） and Tongcheng pigs （obese-type） （described as T33, T65 and T90）. The CRABPI gene was mapped to chromosome 7ql 1-q23 and closely linked to the microsatellite marker SWR1928. Quantitative real-time PCR showed that CRABP1 mRNA was highly expressed in lung and stomach, moderately expressed in placenta and uterus, and weakly expressed in other tissues. Moreover, CRABP1 gene was down-regulated during prenatal skeletal muscle development in both Landrace and Tongcheng pigs and it was expressed much higher in T33 than L33. Two single-nucleotide polymorphisms （SNPs） were detected by sequencing and mass spectrometry methods, allele frequency analysis indicated that g. 281 （G〉A） and g. 2992 （G〉A）were deviated from Hardy-Weinberg equilibrium in the Landrace and DLY （Duroc×（Landrace×Yorkshire）） pig breeds.

ANALYZING HLA HAPLOTYPE OF THE LOCI HLA-A,-B, AND-DRB1 IN MONGOLIA ETHNIC GROUP

Objective To investigate HLA-A,-B and -DRB1 allele and HLA-A-B-DRB1 haplotype frequencies in Mongolia ethnic group. Methods HLA-A, -B, -DRB1 allele and haplotype in the Mongolia ethnic group were investigated based on 93 individuals by PCR- sequence-based typing (SBT) method. Results Twenty-one alleles were detected for HLA-A, 44 for HLA-B, and 26 for HLA-DRB1. The most frequent alleles were HLA-A*2402(0.2097), HLA-B*1302(0.0699), and HLA-DRB1*0701(0.1237). The most common HLA-A-B-DRB1 haplotype were A*3001-B*1302-DRB1*0701, A*0101-B*3701-DRB1*1001, followed by the A*0201-B*4601-DRB1*0901, A*2402-B*4801-DRB1*1101, A*2402-B*5201-DRB1*1501, A*3201-B*3503-DRB1*1301, and A*3303-B*5801-DRB1*0301, which were also presented in Chinese populations. Conclusion The data can be used in forensic and paternity tests to estimate the frequency of a DNA profile or anthropologic research. The characteristics of the distribution of HLA alleles revealed that Mongolia ethnic group is characterized by northern Mongolian Chinese.

Genotypes and polymorphisms of mutant CCR5-△32,CCR2-64I and SDF1-3'A HIV-1 resistance alleles in indigenous Han Chinese

Objective To evaluate the frequencies and polymorphisms of CCR5-△32,CCR2-641 and SDF1-3'A alleles conferring resistance to HIV-1 infection in Chinese population from Han ethnic origin.Methods This cohort was comprised of 1251 subjects(915 men and 336 women)aged 15 -80 years and none was HIV-1 positive.Genotyping of allelic CCR5-△32,CCR2-641 and SDF1-3' A variants was performed using PCR or PCR/RFLP assay,and further confirmed by direct DNA sequencing.Results Our finding shows that the△32 deletion mutation in the CCR5 gene does occur in this population and can be inherited in a Mendelian fashion in indigenous Han Chinese at a very low frequency of 0.00119(n= 1254).The frequencies of mutant CCR2-641 and SDF1-3'A alleles were 0.20023(n = 1251)and 0.2873(n = 893),in this population,which are higher than those found in American Caucasians.Furthermore the polymorphisms of CCR2-641 and SDF1-3' A alleles in the Han Chinese population were different from those in American Caucasians.Statistical analysis showed that the genotype distribution of CCR5-△32,CCR2-641 and SDF1-3' A alleles was in equilibrium according to the Hardy-Weinberg equation.Conclusion The CCR5-△32 mutation may not be a major resistant factor against HIV-1 infection in indigenous Han Chinese.The significance of higher frequencies of CCR2-641 and SDF1-3' A alleles (0.20023 and 0.2791)in the Han population remains to be clarified in HIV-1-positive carriers and AIDS patients.

Prevalence and gene frequency of color vision impairments among children of six populations from North Indian region

X-linked redegreen color blindness is the most widespread form of vision impairment.The study aimed to determine the prevalence and gene frequencies of redegreen color vision impairments among children of six different human populations of Jammu province.A total of 1028 healthy subjects(6e15 years of age)were selected from five Muslim populations and the color vision impairments were determined using the Ishihara’s test of color deficiency.The gene frequency was calculated using HardyeWeinberg equilibrium method.The prevalence of color vision deficiency(CVD)ranged from 5.26%to 11.36%among males and 0.00%e3.03%among females of six different populations.The gender based differences in the frequency of CVD was found to be statistically significant(p<0.0001),with a higher prevalence among male(7.52%)as compared to female(0.83%)children.We observed high frequency of deutan as compared to protan defects.The incidences of deuteranomaly(5.68%)and deuteranopia(2.27%)were higher among male children of Syed population while the frequencies of protanomaly(1.94%),protanopia(1.28%)and achromacy(2.27%)were the highest among male subjects of Khan,Malik and Syed populations,respectively.The allele and genotype frequencies showed cogent differences among six populations.The population based assessment of CVDs help patients to follow adaptive strategies that could minimize the risks of the disease.

β-fibrinogen gene -455A/G polymorphism and plasma fibrinogen level in Chinese stroke patients

Abstract Objectives To investigate the relationship between the β-fibrinogen gene -455A/G polymorphism and plasma fibrinogen level and to determine the influence of the mutation on ischemic stroke. Methods Ninety-one patients (63.5±10.1 years) with ischemic stroke and 74 elderly control subjects (60.6±10.8 years) without any thromboembolic events and 98 healthy blood donators as young control (37.5±13.3 years) were enrolled in this trial. The β-fibrinogen gene -455A/G polymorphism was analyzed for all subjects by PCR-RFLP with the restrictive enzyme Hae Ⅲ, while plasma fibrinogen levels were obtained from the prothrombin time (PT) assay. For statistical analysis, the parameters were compared between any two different groups by the unpaired Student’s t test and the Chi-square test. Before analysis, log transformations for concentrations of fibrinogen were carried out.Results H2 allele frequency was higher in male ischemic stroke patients than in the elderly control (22.7% vs 7.1%, χ 2=5.56, P【0.02). There was no significant difference between the female groups. In those patients without any thromboembolic events (both elderly and young control groups), the frequency of H2 decreased with age (≤40, 21.3%; 41-59, 15.4%; and ≥60, 10.2%). In the male elderly and young control groups, the level of plasma fibrinogen was lower in the H1H1 genotype (287±96*!mg/dl and 234±58*!mg/dl) than in H1H2 and H2H2 (331±44*!mg/dl and 307±55*!mg/dl; t=2.53 and 9.67, P【0.05). In the female elderly groups, this tendency was not found.Conclusion Plasma fibrinogen expression is affected by the β-fibrinogen gene -455A/G polymorphism, and the H2 allele may be a risk factor for ischemic stroke in Chinese males.

Polymorphism analysis of the ABCA3 gene： association with neonatal respiratory distress syndrome in preterm infants

Background Previous reports indicated that mutations in the adenosine triphosphate （ATP）-binding cassette transporter A3 （ABCA3） cause fatal respiratory failure in term infants, and common ABCA3 gene polymorphisms have been characterized at the population level in Caucasians. But the role of ABCA3 in relation to respiratory distress syndrome （RDS） in newborns has not been evaluated within a Chinese population. The aim of this study was to analyze eight single-nucleotide polymorphisms （SNPs） of the ABCA3 gene, and to assess the ABCA3 gene as a candidate gene for susceptibility to RDS in newborns.Methods Eight SNPs were selected and genotyped in 203 newborns. The data analysis and statistical tests were used for allele frequencies, haplotype and Hardy-Weinberg equilibrium pairwise linkage disequilibrium measures. Results There was a haplotype association with SNP rs313909 and SNP rs170447, but no haplotype association was observed among the newborns with and without RDS （P 〉0.05）. The minor allele frequency （G） of the coding SNP （cSNP） rs323043 （P585P） was significantly increased in preterm infants with RDS.Conclusion There is an association between a synonymous cSNP rs323043 and the development of RDS.

The evolution of Hessian fly from the Old World to the New World： Evidence from molecular markers

Eighteen polymorphic microsatellite loci and 11 single-nucleotide polymor- phisms were genotyped in 1 095 individual Hessian fly specimens representing 23 popula- tions from North America, southern Europe, and southwest Asia. The genotypes were used to assess genetic diversity and interrelationship of Hessian fly populations. While phyloge- netic analysis indicates that the American populations most similar to Eurasian populations come from the east coast of the United States, genetic distance is least between （Alabama and California） and （Kazakhstan and Spain）. Allelic diversity and frequency vary across North America, but they are not correlated with distance from the historically documented point of introduction in New York City or with temperature or precipitation. Instead, the greatest allelic diversity mostly occurs in areas with Mediterranean climates. The mi- crosatellite data indicate a general deficiency for heterozygotes in Hessian fly. The North American population structure is consistent with multiple introductions, isolation by dis- tance, and human-abetted dispersal by bulk transport of puparia in infested straw or on harvesting equipment.

Status of Cry1Ac and Cry2Ab2 resistance in field populations of Helicoverpa zea in Texas, USA

Helicoverpa zea is a major target pest of Bt corn and Bt cotton.Field-evolved resistance of H.zea to Cry1 and Cry2 proteins has been widely reported in the United States.Understanding the frequency of resistance alleles in a target insect is critical for Bt resistance management.Despite multiple cases of practical resistance to Cry proteins having been documented in H.zea,there are no data on the current status of alleles conferring resistance to Cry1Ac and Cry2Ab2 in field populations of this pest.During 2018‒2019,a total of 106 F2 families for Cry1Ac and 120 F2 families for Cry2Ab2 were established using mass mating and light trap strategy.We screened 13,568 and 15,360 neonates using a discriminatory dose of Cry1Ac and Cry2Ab2,respectively.The results showed that 93.4%and 35.0%of the F2 families could survive on the discriminatory dose of Cry1Ac and Cry2Ab2,respectively.The estimated resistance allele frequency for Cry1Ac in H.zea ranged from 0.4150 to 0.4975 and for Cry2Ab2 ranged from 0.1097 and 0.1228.These data indicate that the frequency of alleles conferring resistance to Cry1 and Cry2 proteins in H.zea in Texas are high.In addition,our data suggest the resistance to Cry1Ac and Cry2Ab2 in the screened families of H.zea varies from recessive to dominant.The information in this study provides precise estimates of Cry resistance allele frequencies in H.zea and increases our understanding of the risks to the sustainability of Bt crops.