A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis

BACKGROUND AIMS

Previous genome-wide association studies (GWAS) have indicated the involvement of shared (population-non-specific) and non-shared (population-specific) susceptibility genes in the pathogenesis of primary biliary cholangitis (PBC) among European and East-Asian populations. Although a meta-analysis of these distinct populations has recently identified more than 20 novel PBC susceptibility loci, analyses of population-specific genetic architecture are still needed for a more comprehensive search for genetic factors in PBC.

APPROACH RESULTS

Protein tyrosine phosphatase non-receptor type 2 (PTPN2) was identified as a novel PBC susceptibility gene locus through a GWAS and subsequent genome-wide meta-analysis involving 2,181 cases and 2,699 controls from the Japanese population (GWAS-lead variant: rs8098858, p=2.6×10-8). In-silico and in-vitro functional analyses indicated that the risk allele of rs2292758, which is a primary functional variant, decreases PTPN2 expression by disrupting Sp1 binding to the PTPN2 promoter in T follicular helper cells (Tfh) and plasmacytoid dendritic cells (pDCs). Infiltration of PTPN2-positive T-cells and pDCs were confirmed in the portal area of the PBC-liver by immunohistochemistry. Furthermore, transcriptomic analysis of PBC-liver samples indicated the presence of a compromised negative feedback loop in-vivo between PTPN2 and IFNG in patients carrying the risk allele of rs2292758.

CONCLUSIONS

PTPN2, a novel susceptibility gene for PBC in the Japanese population, may be involved in the pathogenesis of PBC via an insufficient negative feedback loop caused by the PTPN2 risk allele of rs2292758 in IFN signaling. This suggests that PTPN2 could be a potential molecular target for PBC treatment.

Incidence and causative agent distribution of viral-induced paediatric asthma exacerbations under strict infection control measures: a single-centre retrospective study in Japan

BACKGROUND

The prevalence of respiratory viruses in children changed under strict infection control measures during the coronavirus disease 2019 (COVID-19) outbreak. In this study, we investigated the frequency of viral detection in the nasopharynx of paediatric patients with asthma exacerbations requiring hospitalization during the COVID-19 pandemic, as well as the distribution of causative viruses.

METHODS

We included paediatric patients admitted for asthma exacerbations between November 2020 and December 2022 at a single centre in Kobe, Japan. Demographic, clinical, and laboratory data were collected from their medical records and using additional questionnaires. All patients enrolled in this study met the diagnostic criteria for asthma exacerbations outlined in the Japanese Pediatric Guideline for the Treatment and Management of Bronchial Asthma 2020. Statistical differences were calculated using univariate analyses (chi-square or Mann‒Whitney U test).

RESULTS

We enrolled 203 children hospitalized for asthma attacks and collected nasopharyngeal samples from 189 patients. The median patient age was 3.0 years. Asthma severity was classified as mild (4.0%), moderate (82.3%), or severe (13.8%). The proportion of viral respiratory infections was 95.2% (180/189). The rate of patients with multiple viral infections was 20.6% (39/189). The most frequently detected pathogens were rhinovirus and enterovirus (RV/EV) at 69.3% (131/189), allowing for duplicate detection, followed by respiratory syncytial virus (RSV) at 28.6% (54/189). We also detected RV/EV almost every month compared to RSV and other viruses. In addition, RV/EV-positive patients were significantly older (p = 0.033), exhibited higher WBC counts (p < 0.001) and higher Eos counts (p < 0.001), had elevated total IgE levels (p < 0.001) and house dust mite-specific IgE levels (p = 0.019), had a shorter duration of hospitalization (p < 0.001), and had a shorter duration of oxygen therapy (p < 0.001). In patients positive for RV/EV, the use of ICSs significantly reduced the severity of the condition (p < 0.001).

CONCLUSION

Even under strict infection control measures, respiratory viruses were detected in the nasopharynx of almost all paediatric patients who had asthma exacerbations requiring hospitalization.

Single-step genomic predictions for heat tolerance of production yields in US Holsteins and Jerseys

The physiological stress caused by excessive heat affects dairy cattle health and production. This study sought to investigate the effect of heat stress on test-day yields in US Holstein and Jersey cows and develop single-step genomic predictions to identify heat tolerant animals. Data included 12.8 million and 2.1 million test-day records, respectively, for 923,026 Holstein and 153,710 Jersey cows in 27 US states. From 2015 through 2021, test-day records from the first 5 lactations included milk, fat, and protein yields (kg). Cow records were included if they had at least 5 test-day records per lactation. Heat stress was quantified by analyzing the effect of a 5-d hourly average temperature-humidity index (THI5d¯) on observed test-day yields. Using a multiple trait repeatability model, a heat threshold (THI threshold) was determined fowr each breed based on the point that the average adjusted yields started to decrease, which was 69 for Holsteins and 72 for Jerseys. An additive genetic component of general production and heat tolerance production were estimated using a multiple trait reaction norm model and single-step genomic BLUP methodology. Random effects were regressed on a function of 5-d hourly average (THI5d¯) and THI threshold. The proportion of test-day records that occurred on or above the respective heat thresholds was 15% for Holstein and 10% for Jersey. Heritability of milk, fat, and protein yields under heat stress for Holsteins increased, with a small standard error, indicating that the additive genetic component for heat tolerance of these traits was observed. This was not as evident in Jersey traits. For Jersey, the permanent environment explained the same or more of the variation in fat and protein yield under heat stress indicating that nongenetic factors may determine heat tolerance for these Jersey traits. Correlations between the general genetic merit of production (in the absence of heat stress) and heat tolerance genetic merit of production traits were moderate in strength and negative. This indicated that selecting for general genetic merit without consideration of heat tolerance genetic merit of production may result in less favorable performance in hot and humid climates. A general genomic estimated breeding value for genetic merit and a heat tolerance genomic estimated breeding value were calculated for each animal. This study contributes to the investigation of the impact of heat stress on US dairy cattle production yields and offers a basis for the implementation of genomic selection. The results indicate that genomic selection for heat tolerance of production yields is possible for US Holsteins and Jerseys, but a study to validate the genomic predictions should be explored.

Nonparallel genome changes within subpopulations over time contributed to genetic diversity within the US Holstein population

Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, and females measured for type traits within the last 2 yr of data. K-means clustering with 5 clusters (C1, C2, C3, C4, and C5) was applied to the genomic relationship matrix based on 58,990 SNP markers to stratify the selected candidates into subpopulations. The general higher inbreeding resulting from within-cluster mating than across-cluster mating suggests the successful stratification into genetically different groups. The largest cluster (C4) contained animals that were less related to each animal within and across clusters. The average fixation index was 0.03, indicating that the populations were differentiated, and allele differences across the subpopulations were not due to drift alone. Starting with the selected candidates within each cluster, a family unit was identified by tracing back through the pedigree, identifying the genotyped ancestors, and assigning them to a pseudogeneration. Each of the 5 families (F1, F2, F3, F4, and F5) was traced back for 10 generations, allowing for changes in frequency of individual SNPs over time to be observed, which we call allele frequencies change. Alternative procedures were used to identify SNPs changing in a parallel or nonparallel way across families. For example, markers that have changed the most in the whole population, markers that have changed differently across families, and genes previously identified as those that have changed in allele frequency. The genomic trajectory taken by each family involves selective sweeps, polygenic changes, hitchhiking, and epistasis. The replicate frequency spectrum was used to measure the similarity of change across families and showed that populations have changed differently. The proportion of markers that reversed direction in allele frequency change varied from 0.00 to 0.02 if the rate of change was greater than 0.02 per generation, or from 0.14 to 0.24 if the rate of change was greater than 0.005 per generation within each family. Cluster-specific SNP effects for stature were estimated using only females and applied to obtain indirect genomic predictions for males. Reranking occurs depending on SNP effects used. Additive genetic correlations between clusters show possible differences in populations. Further research is required to determine how this knowledge can be applied to maintain diversity and optimize selection decisions in the future.

[Short Term and Long Term Outcomes of Robotic Surgery in Sphincter Function Preserving Surgery for Lower Rectal Cancer]

BACKGROUND

Surgical and oncological outcomes of lower rectal cancer remain unsatisfactory. We investigated the short term and long term outcomes of robotic surgery for sphincter function-preserving surgery(SPS)for lower rectal cancer.

METHOD

433 lower rectal cancer patients who underwent SPS at our institution from January 2000 to July 2021 were included, excluding Stage Ⅳ cases and patients with multiple cancers. There were 288 cases of laparotomy, 81 cases of laparoscopic surgery, and 64 cases of robotic surgery; we abbreviated the group names as: OP, LAP, and R, respectively. We retrospectively reviewed the anastomotic leakage rate and prognosis of these groups.

RESULTS

The anastomotic leakage rate was 23.6% in the OP group, 17.3% in the LAP group, and 6.3% in the R group, with a significant difference between the OP group and the R group. The 3-year recurrence free survival rate was 86.7% in the LAP group and 95.6% in the R group. Although there was no significant difference, the prognosis tended to be better in the R group. Local recurrence was observed in 3 patients in the LAP group and 1 patient in the R group.

CONCLUSION

In SPS for advanced lower rectal cancer, robotic surgery may contribute to a reduction in anastomotic leakage.

Dosimetry of Occupational Eye Lens Dose Using a Novel Direct Eye Dosimeter, DOSIRIS, during Interventional Radiology Procedures

In response to the recommendation by the International Commission on Radiological Protection to lower the equivalent eye dose limit, the Japanese Government in April 2021 lowered the equivalent dose limit for the eye lens for occupational exposure. A considerable number of interventional radiology operators are exposed to levels above the new limit. For this reason, a need exists to more accurately evaluate eye lens dose in interventional radiology operators by using a novel direct eye dosimeter, the DOSIRIS™(IRSN, France), which is capable of measuring a 3-mm dose equivalent under protective glasses. The DOSIRIS is a thermoluminescent dosimeter that exhibits good energy dependence and better directional properties than other dosimeters. Dosimetry using DOSIRIS might be accurate and compatible with the latest regulations.

Prognosis of patients with liver cirrhosis: A multi-center retrospective observational study

AIM

Despite advances in the management of liver diseases and changes in the etiology of cirrhosis, few studies have updated the prognosis of cirrhosis. This study aimed to clarify the recent prognosis of cirrhosis and identify risk factors for death.

METHODS

In this retrospective observational study by the Hepatic Disease Network of the National Hospital Organization in Japan, chart reviews were performed to follow patients with cirrhosis beginning in 2011. We conducted Kaplan-Meier survival time analyses stratified by Child-Pugh classification and albumin-bilirubin grade. Cox regression analysis was used to identify risk factors for death.

RESULTS

We identified 444 eligible patients from 25 hospitals, including 303 (68%), 110 (25%), and 31 (7%) patients with Child-Pugh classes A, B, and C, respectively. Hepatitis C virus infection was the cause of cirrhosis for 63% of the patients. The 1-year and 5-year cumulative survival rates of patients with Child-Pugh classes A, B, and C were 90% and 61%, 78% and 42%, and 65% and 25%, respectively. The 1-year and 5-year cumulative survival rates of patients with albumin-bilirubin grades 1, 2, and 3 were 98% and 80%, 91% and 56%, and 58% and 23%, respectively. Cirrhosis classification (Child-Pugh and albumin-bilirubin), age, liver cancer, and untreated esophageal varices were associated with increased hazard of death.

CONCLUSIONS

Little improvement was observed in the prognosis of cirrhosis compared with previous reports, and the prognosis of Child-Pugh class C cirrhosis remained poor. Untreated esophageal varices were identified as a risk factor for death.

Reducing computational cost of large-scale genomic evaluation by using indirect genomic prediction

Over half a million Holsteins are being genotyped annually in the United States. The computational cost of including all genotypes in single-step genomic (ssG)BLUP is high, although it is feasible to conduct large-scale genomic prediction using an efficient algorithm such as APY (algorithm for proven and young). An effective method to further reduce the computing cost could be the use of indirect genomic predictions (IGP) for genotyped animals when they have neither progeny nor phenotypes. These young genotyped animals have no effect on the other genotyped animals and could have their genomic prediction done indirectly. The main objective of this study was to calculate IGP for various groups of genotyped animals and investigate the reduction in computing time as well as bias and accuracy of the IGP. We compared IGP with genomic (G)EBV for 18 linear type traits in US Holsteins, including 2.3 million (M) genotyped animals. The full data set consisted of 10.9M records for 18 linear type traits up to 2018 calving, 13.6M animals in the pedigree, and 2.3M animals genotyped for 79K SNP. For IGP, ssGBLUP included all genotyped animals except those with neither progeny nor phenotypes by year from 2014 to 2018 (i.e., the target animals). The SNP marker effects were computed based on GEBV for genotyped animals that had progeny, or phenotypes, or both. Further, IGP were calculated for target genotyped animals in each year group. For all genotyped animal groups from 2014 to 2018, the coefficients of determination (R²) of a linear regression of GEBV on IGP were 0.960 for males and 0.954 for females for 18 traits on average. To reduce computing costs, the SNP marker effects were calculated based on GEBV from randomly selected genotyped animals from 15K to 60K. By randomly selecting a small number of genotyped animals, the computing time was dramatically reduced. As more genotyped animals were randomly selected to calculate SNP effects, R² was higher (more accurate) and the regression coefficient was lower (more inflated IGP). In a practical genomic evaluation in US Holsteins, to get sufficient contributions from GEBV, 25K to 35K is a rational number of genotyped animals that can be randomly selected to compute SNP effects and obtain accurate and unbiased IGP. Considering the computing time and both unbiasedness and accuracy of IGP, genomic evaluation can be conducted separately in GEBV for genotyped animals with phenotypes or progeny and in IGP for young genotyped animals. This can be a practical solution when conducting a large-scale genomic evaluation and would enable more frequent evaluation at lower cost, especially when many genotyped animals have neither phenotypes nor progeny.

Genomic predictions for yield traits in US Holsteins with unknown parent groups

The objective of this study was to assess the reliability and bias of estimated breeding values (EBV) from traditional BLUP with unknown parent groups (UPG), genomic EBV (GEBV) from single-step genomic BLUP (ssGBLUP) with UPG for the pedigree relationship matrix (A) only (SS_UPG), and GEBV from ssGBLUP with UPG for both A and the relationship matrix among genotyped animals (A₂₂; SS_UPG2) using 6 large phenotype-pedigree truncated Holstein data sets. The complete data included 80 million records for milk, fat, and protein yields from 31 million cows recorded since 1980. Phenotype-pedigree truncation scenarios included truncation of phenotypes for cows recorded before 1990 and 2000 combined with truncation of pedigree information after 2 or 3 ancestral generations. A total of 861,525 genotyped bulls with progeny and cows with phenotypic records were used in the analyses. Reliability and bias (inflation/deflation) of GEBV were obtained for 2,710 bulls based on deregressed proofs, and on 381,779 cows born after 2014 based on predictivity (adjusted cow phenotypes). The BLUP reliabilities for young bulls varied from 0.29 to 0.30 across traits and were unaffected by data truncation and number of generations in the pedigree. Reliabilities ranged from 0.54 to 0.69 for SS_UPG and were slightly affected by phenotype-pedigree truncation. Reliabilities ranged from 0.69 to 0.73 for SS_UPG2 and were unaffected by phenotype-pedigree truncation. The regression coefficient of bull deregressed proofs on (G)EBV (i.e., GEBV and EBV) ranged from 0.86 to 0.90 for BLUP, from 0.77 to 0.94 for SS_UPG, and was 1.00 ± 0.03 for SS_UPG2. Cow predictivity ranged from 0.22 to 0.28 for BLUP, 0.48 to 0.51 for SS_UPG, and 0.51 to 0.54 for SS_UPG2. The highest cow predictivities for BLUP were obtained with the most extreme truncation, whereas for SS_UPG2, cow predictivities were also unaffected by phenotype-pedigree truncations. The regression coefficient of cow predictivities on (G)EBV was 1.02 ± 0.02 for SS_UPG2 with the most extreme truncation, which indicated the least biased predictions. Computations with the complete data set took 17 h with BLUP, 58 h with SS_UPG, and 23 h with SS_UPG2. The same computations with the most extreme phenotype-pedigree truncation took 7, 36, and 15 h, respectively. The SS_UPG2 converged in fewer rounds than BLUP, whereas SS_UPG took up to twice as many rounds. Thus, the ssGBLUP with UPG assigned to both A and A₂₂ provided accurate and unbiased evaluations, regardless of phenotype-pedigree truncation scenario. Old phenotypes (before 2000 in this data set) did not affect the reliability of predictions for young selection candidates, especially in SS_UPG2.

[NEED FOR SUBCUTANEOUS IMMUNOTHERAPY IN PEDIATRIC PATIENTS WITH ALLERGIC RHINITIS AFTER THE EXPANDED INDICATION FOR SUBLINGUAL IMMUNOTHERAPY]

BACKGROUND

Although the indication for sublingual immunotherapy (SLIT) was expanded in pediatric patients with allergic rhinitis in recent years, some patients choose subcutaneous immunotherapy (SCIT).

OBJECTIVE

The objective of this study was to investigate the reason why they chose SCIT in spite of injection pain and high risk of systemic reaction.

METHODS

The subjects were 58 patients who diagnosed with allergic rhinitis and introduced SCIT at our hospital between June 2018 and January 2021. The reasons why they chose SCIT were collected from medical records.

RESULT

The median age at the start of treatment was 9 years 0 months. The most common reason why they chose SCIT was "difficult to maintain adherence of SLIT" in 28 cases (48%). Other reasons were as follows: "side effects of SLIT", "expectation for the effect of SCIT", "young age (under 5 years old)" and "motivation for allergic disease treatment".

CONCLUSION

Two-thirds of the reasons why they chose SCIT were because it was difficult to continue SLIT for some reasons.

Bias in genomic predictions by mating practices for linear type traits in a large-scale genomic evaluation

The objective of this study was to clarify how bias in genomic predictions is created by investigating a relationship among selection intensity, a change in heritability (Δh²), and assortative mating (ASM). A change in heritability, resulting from selection, reflects the impact that the Bulmer effect has on the reduction in between-family variation, whereas assortative mating impacts the within-family variance or Mendelian sampling variation. A partial data set up to 2014, including 841K genotyped animals, was used to calculate genomic predictions with a single-step genomic model for 18 linear type traits in US Holsteins. A full data set up to 2018, including 2.3 million genotyped animals, was used to calculate benchmark genomic predictions. Inbreeding and unknown parent groups for missing parents of animals were included in the model. Genomic evaluation was performed using 2 different genetic parameters: those estimated 14 yr ago, which have been used in the national genetic evaluation for linear type traits in the United States, and those newly estimated with recent records from 2015 to 2018 and those corresponding pedigrees. Genetic trends for 18 type traits were estimated for bulls with daughters and cows with phenotypes in 2018. Based on selection intensity and mating decisions, these traits can be categorized into 3 groups: (a) high directional selection, (b) moderate selection, and (c) intermediate optimum selection. The first 2 categories can be explained by positive assortative mating, and the last can be explained by negative assortative or disassortative mating. Genetic progress was defined by genetic gain per year based on average standardized genomic predictions for cows from 2000 to 2014. Traits with more genetic progress tended to have more "inflated" genomic predictions (i.e., "inflation" means here that genomic predictions are larger in absolute values than expected, whereas "deflation" means smaller than expected). Heritability estimates for 14 out of 18 traits declined in the last 16 yr, and Δh² ranged from -0.09 to 0.04. Traits with a greater decline in heritability tended to have more deflated genomic predictions. Biases (inflation or deflation) in genomic predictions were not improved by using the latest genetic parameters, implying that bias in genomic predictions due to preselection was not substantial for a large-scale genomic evaluation. Moreover, the strong selection intensity was not fully responsible for bias in genomic predictions. The directional selection can decrease heritability; however, positive assortative mating, which was strongly associated with large genetic gains, could minimize the decline in heritability for a trait under strong selection and could affect bias in genomic predictions.

A woman with a dual genetic diagnosis of autosomal dominant tubulointerstitial kidney disease and KBG syndrome

We present a female patient with a dual genetic diagnosis of autosomal dominant tubulointerstitial kidney disease and KBG syndrome. The proband was an 18-year-old woman presenting with intellectual disability, renal insufficiency, and hyperuricemia. Abdominal ultrasonography did not reveal any abnormalities. The patient's father had been diagnosed with chronic kidney disease and hyperuricemia in his twenties; however, he had no intellectual disability. Her mother and two younger siblings were not affected. Next generation sequencing (NGS) identified mutations in UMOD (c.796T > C) of the proband and her father, and in ANKRD11 (c.1903_1907del) of the proband. Renal insufficiency and intellectual disability were attributed to mutations in UMOD and ANRKD11, respectively. When making genetic diagnoses, the presence of multiple mutations in an individual should be considered, particularly when not all symptoms could be attributed to a single disease. The number of patients with dual genetic diagnosis is expected to increase as NGS becomes more readily available; thus, making it necessary to undertake a careful and robust assessment of the clinical symptoms and the related genotypes, to ensure an accurate diagnosis.

Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis

Genome‐wide association studies (GWASs) in European and East Asian populations have identified more than 40 disease‐susceptibility genes in primary biliary cholangitis (PBC). The aim of this study is to computationally identify disease pathways, upstream regulators, and therapeutic targets in PBC through integrated GWAS and messenger RNA (mRNA) microarray analysis. Disease pathways and upstream regulators were analyzed with ingenuity pathway analysis in data set 1 for GWASs (1,920 patients with PBC and 1,770 controls), which included 261 annotated genes derived from 6,760 single‐nucleotide polymorphisms (P < 0.00001), and data set 2 for mRNA microarray analysis of liver biopsy specimens (36 patients with PBC and 5 normal controls), which included 1,574 genes with fold change >2 versus controls (P < 0.05). Hierarchical cluster analysis and categorization of cell type–specific genes were performed for data set 2. There were 27 genes, 10 pathways, and 149 upstream regulators that overlapped between data sets 1 and 2. All 10 pathways were immune‐related. The most significant common upstream regulators associated with PBC disease susceptibility identified were interferon‐gamma (IFNG) and CD40 ligand (CD40L). Hierarchical cluster analysis of data set 2 revealed two distinct groups of patients with PBC by disease activity. The most significant upstream regulators associated with disease activity were IFNG and CD40L. Several molecules expressed in B cells, T cells, Kupffer cells, and natural killer–like cells were identified as potential therapeutic targets in PBC with reference to a recently reported list of cell type–specific gene expression in the liver. Conclusion: Our integrated analysis using GWAS and mRNA microarray data sets predicted that IFNG and CD40L are the central upstream regulators in both disease susceptibility and activity of PBC and identified potential downstream therapeutic targets.

Intestinal Organoids Generated from Human Pluripotent Stem Cells

The gastrointestinal system is one of the most complex organ systems in the human body, and consists of numerous cell types originating from three germ layers. To understand intestinal development and homeostasis and elucidate the pathogenesis of intestinal disorders, including unidentified diseases, several in vitro models have been developed. Human pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), have remarkable developmental plasticity and possess the potential for a wide variety of applications. Three-dimensional organs, termed organoids and produced in vitro by PSCs, contain not only epithelium but also mesenchymal tissue and partially recapitulate intestinal functions. Such intestinal organoids have begun to be applied in disease models and drug development and have contributed to a detailed analysis of molecular interactions and findings in the synergistic development of biomedicine for human digestive organs. In this review, we describe gastrointestinal organoid technology derived from PSCs and consider its potential applications.

Controlling bias in genomic breeding values for young genotyped bulls

The objectives of this study were to investigate bias in genomic predictions for dairy cattle and to find a practical approach to reduce the bias. The simulated data included phenotypes, pedigrees, and genotypes, mimicking a dairy cattle population (i.e., cows with phenotypes and bulls with no phenotypes) and assuming selection by breeding values or no selection. With the simulated data, genomic estimated breeding values (GEBV) were calculated with a single-step genomic BLUP and compared with true breeding values. Phenotypes and genotypes were simulated in 10 generations and in the last 4 generations, respectively. Phenotypes in the last generation were removed to predict breeding values for those individuals using only genomic and pedigree information. Complete pedigrees and incomplete pedigrees with 50% missing dams were created to construct the pedigree-based relationship matrix with and without inbreeding. With missing dams, unknown parent groups (UPG) were assigned in relationship matrices. Regression coefficients (b₁) and coefficients of determination (R²) of true breeding values on (G)EBV were calculated to investigate inflation and accuracy in GEBV for genotyped animals, respectively. In addition to the simulation study, 18 linear type traits of US Holsteins were examined. For the 18 type traits, b₁ and R² of GEBV with full data sets on GEBV with partial data sets for young genotyped bulls were calculated. The results from the simulation study indicated inflation in GEBV for genotyped males that were evaluated with only pedigree and genomic information under BLUP selection. However, when UPG for only pedigree-based relationships were included, the inflation was reduced, accuracy was highest, and genetic trends had no bias. For the linear type traits, when UPG for only pedigree-based relationships were included, the results were generally in agreement with those from the simulation study, implying less bias in genetic trends. However, when including no UPG, UPG in pedigree-based relationships, or UPG in genomic relationships, inflation and accuracy in GEBV were similar. The results from the simulation and type traits suggest that UPG must be defined accurately to be estimable and inbreeding should be included in pedigree-based relationships. In dairy cattle, known pedigree information with inbreeding and estimable UPG plays an important role in improving compatibility between pedigree-based and genomic relationship matrices, resulting in more reliable genomic predictions.

Disaster preparation: Survey of patients with food allergies in Kobe, Japan

BACKGROUND

Securing food for patients with food allergies may be more difficult during disasters, but reports on the status of household allergen-free food reserves in preparation for disasters are limited. This study investigated the household stock status of allergen-free foods in preparation for disasters in Kobe City after the Great Hanshin-Awaji Earthquake.

METHODS

The survey targets were 172 parents of patients with a food allergy who underwent in-hospital oral food challenge test for allergies at four hospitals from October 2016 to March 2017. Of these, 158 patients with allergies to eggs, milk and wheat were included in the analysis. The first survey was performed to investigate patient characteristics and stockpiling status of allergen-free foods in parallel with oral food challenge tests. The second survey was performed on the follow-up visit to investigate any changes in behavior.

RESULTS

Median patient age was 3 years, with boys comprising 68.4% of the patients. Eggs were the most eliminated food, and the median number of foods avoided was 2. A total of 82.3% of parents had experienced disasters. The proportion of households that stockpiled allergy-free meals was 42.4%, and the median amount was 3 days. The stockpiling situation did not differ according to the parents' disaster experience. In the second survey, 45.3% had modified their stockpiling practice.

CONCLUSIONS

Even in this area where the Great Hanshin-Awaji Earthquake occurred, household stockpiles of allergen-free foods are inadequate; therefore, all medical staff should educate families about the necessity of stocking allergen-free food for disasters.

Single-step genome-wide association for longitudinal traits of Canadian Ayrshire, Holstein, and Jersey dairy cattle

Estimating single nucleotide polymorphism (SNP) effects over time is essential to identify and validate candidate genes (or quantitative trait loci) associated with time-dependent variation of economically important traits and to better understand the underlying mechanisms of lactation biology. Therefore, in this study, we aimed to estimate time-dependent effects of SNP and identifying candidate genes associated with milk (MY), fat (FY), and protein (PY) yields, and somatic cell score (SCS) in the first 3 lactations of Canadian Ayrshire, Holstein, and Jersey breeds, as well as suggest their potential pattern of phenotypic effect over time. Random regression coefficients for the additive direct genetic effect were estimated for each animal using single-step genomic BLUP, based on 2 random regression models: one considering MY, FY, and PY in the first 3 lactations and the other considering SCS in the first 3 lactations. Thereafter, SNP solutions were obtained for random regression coefficients, which were used to estimate the SNP effects over time (from 5 to 305 d in lactation). The top 1% of SNP that showed a high magnitude of SNP effect in at least 1 d in lactation were selected as relevant SNP for further analyses of candidate genes, and clustered according to the trajectory of their SNP effects over time. The majority of SNP selected for MY, FY, and PY increased the magnitude of their effects over time, for all breeds. In contrast, for SCS, most selected SNP decreased the magnitude of their effects over time, especially for the Holstein and Jersey breeds. In general, we identified a different set of candidate genes for each breed, and similar genes were found across different lactations for the same trait in the same breed. For some of the candidate genes, the suggested pattern of phenotypic effect changed among lactations. Among the lactations, candidate genes (and their suggested phenotypic effect over time) identified for the second and third lactations were more similar to each other than for the first lactation. Well-known candidate genes with major effects on milk production traits presented different suggested patterns of phenotypic effect across breeds, traits, and lactations in which they were identified. The candidate genes identified in this study can be used as target genes in studies of gene expression.

[DIFFERENCE BETWEEN STANDARDIZED MITE ANTIGEN AND HOUSE DUST EXTRACT IN RUSH SUBCUTANEOUS IMMUNOTHERAPY FOR CHILDREN]

RATIONALE

Standardized allergen extracts are recommended for allergen immunotherapy. Since 2015, for patients with house dust mite allergies, we used a standardized house dust mite extract for subcutaneous immunotherapy, rather than non-standardized house dust extract. This study hypothesizes that standardized house dust mite extract (HDM group) was superior to non-standardized house dust extract (HD group) for subcutaneous immunotherapy.

METHODS

In this noninterventional, retrospective study, we enrolled patients with allergic rhinitis and sensitization to house dust mites. The HDM group (27 patients) received subcutaneous standardized extract immunotherapy since 2015, and the HD group (37 patients) received non-standardized extracts before 2015. We assessed the safety and efficacy between the two groups; the safety was assessed by the systemic reaction (SR) rate. The efficacy was assessed by reductions in the allergic rhinitis symptom-medication score, and the asthma treatment score, over a year.

RESULTS

The SR rate of the HDM group (44%) was significantly higher than that (14%) of the HD group. The HDM group displayed a 57% reduction in the allergic rhinitis symptom-medication score, which was markedly higher than the 40% reduction observed in the HD group. In the standardized group, there was a 66% reduction occurred in the asthma medication score, markedly higher than the 36% reduction observed among patients in the HD group.

CONCLUSIONS

Standardized house dust mite extract was more effective than non-standardized house dust extract for subcutaneous immunotherapy; however, the establishment of safer methods is warranted.

[Laparoscopic Gastrectomy for Early Gastric Cancer in a Patient with an Adachi Type Ⅵ Arterial Variant-A Case Study]

We report successfull aparoscopic distalgastrectomy in a patient with early gastric cancer and an Adachi type Ⅵ arterial variant. The case is a male in his 50's who was detected a type 0-Ⅱc lesion on the antrum of the stomach and diagnosed as tub2. Laparoscopic distalgastrectomy was performed, with the pathologic diagnosis of cT1bN0M0, cStage Ⅰ. MD-CT showed absence of the common hepatic artery ventralto the portalvein, consistent with an Adachi type Ⅵ arterialvariant. The interface between pancreatic and fatty tissue was separated in suprapancreatic dissection, and was extended between the hepatoduodenal ligament and splenic artery, with exposure of the surface of the portal vein. Thus, safe dissection of No. 8a area was achieved. Discussion: Adachi classified the celiac artery branches into 6 types and 28 groups. Type Ⅵ, a variant of the common hepatic artery located on the dorsalaspect of the portalvein, has a reported frequency of 2%. Because it is a variant of the hepatic artery, a landmark of suprapancreatic dissection, careful observation is required to determine the anatomy. Although tactile sensation is limited in laparoscopic surgery, arterial pulsation is clearly visible. To ensure a safe procedure, it is important to identify vesselanatomy both pre- and intraoperatively.

Dual energy CT is useful for the prediction of mesenteric and lateral pelvic lymph node metastasis in rectal cancer

The aim of the present retrospective study was to investigate the predictability of dual-energy computed tomography (DECT) for pararectal lymph node (PRLN) metastasis and lateral pelvic lymph node (LPLN) metastasis in rectal cancer (RC). The present study involved 44 patients with RC who were examined by DECT and then underwent surgery between May 2015 and September 2017. LPLN dissection was performed in 24 patients. The normalized iodine concentration (nIC), the ratio of iodine concentration in the lymph node (LN) to that in the common iliac artery on DECT, of the largest PRLN and LPLN was calculated, and the association between LN metastasis and nIC was analyzed. The median nIC value for PRLNs was significantly lower in PRLN metastasis-positive cases compared with PRLN metastasis-negative cases in the arterial phase [0.18 vs. 0.25; P=0.01; cut-off, 0.24; area under the curve (AUC), 0.733] and portal phase (0.47 vs. 0.61; P=0.03; cut-off, 0.59; AUC, 0.701). A significant difference was not identified between the median maximum short axis diameter of PRLNs in PRLN metastasis-positive and metastasis-negative cases (7.6 vs. 6.4 mm; P=0.33). The nIC for LPLNs was not significantly different between LPLN metastasis-positive and metastasis-negative cases in the arterial phase (0.15 vs. 0.21; P=0.19); but was significantly lower in LPLN metastasis-positive cases compared with LPLN metastasis-negative cases in the portal phase (0.29 vs. 0.56; P=0.04; cut-off, 0.29; AUC, 0.877). The maximum short axis diameter of LPLNs was significantly larger in metastasis-positive cases compared with LPLN metastasis-negative cases (9.1 vs. 4.8 mm; P=0.03; cut-off, 7.0 mm; AUC, 0.912). In conclusion, the nIC was identified to be significantly lower in metastasis-positive cases, which may be useful for the prediction of PRLN and LPLN metastases. A combination of size-based diagnosis and DECT may increase the accuracy of preoperative diagnosis.

The geomorphology, color, and thermal properties of Ryugu: Implications for parent-body processes

The near-Earth carbonaceous asteroid 162173 Ryugu is thought to have been produced from a parent body that contained water ice and organic molecules. The Hayabusa2 spacecraft has obtained global multicolor images of Ryugu. Geomorphological features present include a circum-equatorial ridge, east-west dichotomy, high boulder abundances across the entire surface, and impact craters. Age estimates from the craters indicate a resurfacing age of [Formula: see text] years for the top 1-meter layer. Ryugu is among the darkest known bodies in the Solar System. The high abundance and spectral properties of boulders are consistent with moderately dehydrated materials, analogous to thermally metamorphosed meteorites found on Earth. The general uniformity in color across Ryugu's surface supports partial dehydration due to internal heating of the asteroid's parent body.

[A Case of Pancreatic Acinar Cell Carcinoma in a Young Woman without Recurrence after Systemic Chemotherapy Using S-1]

A 26-year-old woman underwent laparoscopic-assisted distal pancreatectomy and splenectomy for a tumor in the tail of the pancreas. Although the preoperative diagnosis was a solid pseudopapillary tumor, pathological tissue examination revealed that the tumor was a pancreatic acinar cell carcinoma. She was treated with S-1 chemotherapy for 6 months without severe side effects, and no recurrence was detected on several imaging inspections. Acinar cell carcinoma of the pancreas is a rare tumor in young patients, and there are few reports of treatment with postoperative chemotherapy.

[A Case of Laparoscopic Resection for Locally Advanced Primary Rectal Cancer after Neoadjuvant Chemotherapy]

We treateda 70-year-oldfemale patient with locally advancedrectal cancer accompaniedby metastases to other organs. Three courses of S-1 plus oxaliplatin(SOX)therapy were administered as neoadjuvant chemotherapy(NAC), andthe cancer was subsequently treatedwith laparoscopic rectal resection. She hadvisiteda physician with a chief complaint of melena. A type 2 tumor located in the rectum Rb was found during the lower gastrointestinal endoscopy, which was diagnosed as an adenocarcinoma by biopsy. Vaginal invasion andlymph node metastasis were observedon CT andMRI. After 3 courses of SOX therapy(NAC), her condition was categorized as SD. Laparoscopic rectal amputation(D3)combinedwith resection of the ovary, uterus, and vagina was performed. On histopathological examination, the tumor was an adenocarcinoma, muc> tub2, ypT4b(AI, vaginal wall), int, INF b, ly1, v2, EX(-), PN1a, grade 1, pPM0, pDM0, pRM0 and pStage Ⅲa. The histological analysis demonstrated that the therapeutic effect of chemotherapy was grade 1a. Laparoscopic surgery, which is a relatively safe procedure, may be useful after NAC for an R0 resection.

[Outcomes of Total Mesorectal Excision and Lateral Lymph Node Dissection following Neoadjuvant Chemotherapy for Lower Rectal Cancer with Lateral Lymph Node Metastasis]

INTRODUCTION

Progressive lower rectal cancer with metastasis to the lateral lymph nodes has poor prognosis, requiring systemic chemotherapy. In addition, because laparoscopic lateral lymph node dissection(LLND)in positive cases of metastasis to the lateral lymph nodes is difficult, it has not been commonly used. Here, we report the treatment results of neoadjuvant chemotherapy(NAC)and subsequent laparoscopic total mesorectal excision(TME)plus LLND in cases of lower rectal cancer with metastasis to the lateral lymph nodes.

SUBJECTS AND METHODS

The subjects were 4 patients with metastasis to the lateral lymph nodes who underwent LLND after NAC. The surgical outcomes were investigated retrospectively.

RESULTS

The mean surgical time was 398 minutes, and the mean bleeding amount was 150 g. In total, 33.5 lymph nodes were dissected, including 15.3 lateral lymph nodes. There was no switch to laparotomy, and no postoperative complications of Grade Ⅲ or higher according to the Clavien-Dindo classification were observed.

CONCLUSION

Laparoscopic TME plus LLND after NAC is considered safe and useful as radical surgery for positive cases of metastasis to the lymph nodes.

Necrotizing fasciitis of the thigh due to penetrated descending colon cancer: a case report

Background

Necrotizing fasciitis (NF) caused by colorectal cancer is rare, and very few cases associated with colon cancer have been reported. We describe the case of a patient with NF in the left thigh due to penetration of descending colon cancer who was treated with one-stage surgical resection without creating a stoma.

Case presentation

An 80-year-old woman was brought to our hospital complaining of fever and difficulty with body movement. A physical examination showed subcutaneous emphysema from the left lower abdomen to the left femoral region. CT showed abscess formation with emphysema around the descending colon, and the wall of the descending colon was thickened, which led to suspicion of colon cancer. The patient was subsequently diagnosed with NF due to penetration of descending colon cancer. Left hemicolectomy and open drainage of the left femoral region was performed. The histopathological findings were well-differentiated adenocarcinoma, with the tumor grown through the serosa (T4a) and with no metastasis to lymph nodes (N0). After surgery, the patient received intensive care for septic shock and lavage of the open drainage site, and sepsis was controlled progressively. After closure of the drainage site, the patient was transferred to a different hospital at 26 days after surgery, and she has had 6-month relapse-free survival.

Conclusions

In NF caused by colon cancer, early one-stage resection may improve the oncological outcome. Physical status should be assessed carefully, and one-stage resection should be considered if the patient has the capacity to undergo this procedure.

Calcifying nested stromal epithelial tumor of the liver in a patient with Klinefelter syndrome: a case report and review of the literature

BACKGROUND

Calcifying nested stromal epithelial tumor (CNSET) is a primary neoplasm of the liver, characterized by well-demarcated nests consisting of spindle and epithelioid cells with calcification and bone formation. An association of Cushing syndrome with CNSET has drawn attention, but the origin of CNSET has not been clarified.

CASE PRESENTATION

We report here the case of a 20-year-old male with Klinefelter syndrome who underwent liver resection for an increasing liver tumor that was pathologically diagnosed with CNSET. He was postoperatively followed up and received several examinations, and recurrences and extrahepatic lymph node metastases were detected on the 64th day after surgery. Chemoembolization and chemotherapy were not effective, leading to tumor progression with development of progressive liver failure, and the patient finally died 164 days after hepatectomy.

CONCLUSIONS

This case suggests that an imbalance of hormones affects the genesis and progression of CNSET, and indicates the importance of closely following patients with CNSET by imaging with attention to hepatic recurrence and extrahepatic metastases.

Relationships among mortality, performance, and disorder traits in broiler chickens: a genetic and genomic approach

Four performance-related traits [growth trait (GROW), feed efficiency trait 1 (FE1) and trait 2 (FE2), and dissection trait (DT)] and 4 categorical traits [mortality (MORT) and 3 disorder traits (DIS1, DIS2, and DIS3)] were analyzed using linear and threshold single- and multi-trait models. Field data included 186,596 records of commercial broilers from Cobb-Vantress, Inc. Average-information restricted maximum likelihood and Gibbs sampling-based methods were used to obtain estimates of the (co)variance components, heritabilities, and genetic correlations in a traditional approach using best linear unbiased prediction (BLUP). The ability to predict future breeding values (measured as realized accuracy) was checked in the last generation when traditional BLUP and single-step genomic BLUP were used. Heritability estimates for GROW, FE1, and FE2 in single- and multi-trait models were similar and moderate (0.22 to 0.26) but high for DT (0.48 to 0.50). For MORT, DIS1, and DIS2, heritabilities were 0.13, 0.24, and 0.34, respectively. Estimates from single- and multi-trait models were also very similar. However, heritability for DIS3 was higher from the single-trait threshold model than for the multi-trait linear-threshold model (0.29 vs. 0.19). Genetic correlations between growth traits and MORT were weak, except for maternal GROW, which had a moderate negative correlation (-0.50) with MORT. The genetic correlation between MORT and DIS1 was strong and positive (0.77). Feed efficiency 1, which was moderately heritable (0.25) and is highly selected for, was not genetically related to MORT of broilers and other disorders. Broiler MORT also had moderate heritability (0.13), which suggests that MORT and FE1 can be improved through selection without negatively impacting other important traits. Selection of heavier maternal GROW also may decrease offspring MORT.

Reaction norm for yearling weight in beef cattle using single-step genomic evaluation

When the environment on which the animals are raised is very diverse, selecting the best sires for different environments may require the use of models that account for genotype by environment interaction (G × E). The main objective of this study was to evaluate the existence of G × E for yearling weight (YW) in Nellore cattle using reaction norm models with only pedigree and pedigree combined with genomic relationships. Additionally, genomic regions associated with each environment gradient were identified. A total of 67,996 YW records were used in reaction norm models to calculate EBV and genomic EBV. The method of choice for genomic evaluations was single-step genomic BLUP (ssGBLUP). Traditional and genomic models were tested on the ability to predict future animal performance. Genetic parameters for YW were obtained with the average information restricted maximum likelihood method, with and without adding genomic information for 5,091 animals. Additive genetic variances explained by windows of 200 adjacent SNP were used to identify genomic regions associated with the environmental gradient. Estimated variance components for the intercept and the slope in traditional and genomic models were similar. In both models, the observed changes in heritabilities and genetic correlations for YW across environments indicate the occurrence of genotype by environment interactions. Both traditional and genomic models were capable of identifying the genotype by environment interaction; however, the inclusion of genomic information in reaction norm models improved the ability to predict animals' future performance by 7.9% on average. The proportion of genetic variance explained by the top SNP window was 0.77% for the regression intercept (BTA5) and 0.82% for the slope (BTA14). Single-step GBLUP seems to be a suitable model to predict genetic values for YW in different production environments.

The Prevalence and Implication of Zinc Deficiency in Patients With Chronic Liver Disease

Background

Patients with liver cirrhosis often exhibit zinc deficiency. Although zinc is involved in many bioactivities, many aspects of clinical implications of zinc deficiency in liver cirrhosis remain unclear. We aimed to reveal the prevalence and implications of zinc deficiency in liver cirrhosis by assessing associations with parameters such as clinical symptoms and laboratory data.

Methods

In 235 cirrhosis patients enrolled at multiple medical institutions in 2009, we assessed how blood zinc levels were associated with their clinical symptoms, patients characteristics, and liver function test results.

Results

Blood zinc levels were most strongly correlated with blood albumin levels among the study parameters (r = 0.587, P < 0.0001). When blood albumin levels were ≤ 3.5 g/dL, blood zinc levels were < 70 μg/dL in 88% of patients. Additionally, significant correlations were observed with age (r = -0.253, P = 0.0014), aspartate aminotransferase levels (r = -0.254, P = 0.0020), total bilirubin levels (r = -0.222, P = 0.0053), prothrombin time (r = -0.255, P = 0.0029), branched-chain amino acid to tyrosine ratio (r = 0.357, P < 0.0001), Child-Pugh score (r = 0.469, P < 0.0001), ammonia levels (r = -0.246, P = 0.0028), and total cholesterol levels (r = 0.314, P < 0.0001). Blood zinc levels were significantly lower in patients with edema/ascites (P < 0.0001), those with hepatic encephalopathy (P = 0.0215), those receiving oral diuretics (P = 0.0045), and those receiving oral branched-chain amino acids (P < 0.0001) than in those without these conditions.

Conclusions

Zinc deficiency is prevalent in cirrhosis patients, whereas nitrogen metabolic disorders, particularly hypoalbuminemia, can be an indicator of zinc deficiency. Thus, cirrhosis patients exhibiting a nitrogen metabolic disorder should be examined for the presence of zinc deficiency.

[A Case of Myocardial Metastasis of Esophageal Squamous Cell Carcinoma]

Myocardial metastasis for esophageal squamous cell carcinoma(ESCC)is relatively rare and it is diagnosed as a part of widespread metastasis in the terminal stage. We experienced a case of myocardial metastasis of ESCC treated effectively with chemoradiotherapy. A 56-year-old man was diagnosed ESCC(clinical T3N2M0, Stage III). He received neoadjuvant chemotherapy of 5-fluorouracil plus cisplatin followed by subtotal esophagectomy with dissection of the 3 regional lymph nodes. The pathological diagnosis was moderate differentiated squamous cell carcinoma, CT-pT3(T3), pN1, sM0, fStage III. Four months after surgery, he had no clinical symptom, however myocardial metastasis located in the apex was detected on the follow up positron emission tomography(PET). Chemoradiotherapy was performed for the myocardial metastasis. Myocardial metastasis treated effectively with chemoradiotherapy almost disappeared on the PET and computed tomography taken 3 months after chemoradiotherapy. He died, however, of multiple liver and bone metastases 15 months after the initial surgery.

[The Impact of Neutrophil-Lymphocyte Ratio on the Prognosis in Patients Who Underwent Esophagectomy for Esophageal Cancer]

BACKGROUND

Thene utrophil-lymphocyteratio (NLR)reflects a patient's systemic inflammatory response. Several studies have revealed that the NLR is associated with a poor prognosis in several types of malignant tumors such as colorectal and lung cancer. The aim of this study was to evaluate the impact of preoperative NLR on the prognosis of patients with esophageal cancer.

METHODS

The NLR was calculated for 93 consecutive patients with clinical Stage II or III esophageal cancer, who underwent curative esophagectomy following neoadjuvant chemotherapy between 2011 and 2013. The impact of preoperativeNLR on overall survival(OS)after esophagectomy was evaluated. The NLR cut off value was set to 2.

RESULTS

The 3-year OS of patients with NLR≥2 was significantly shorter than patients with NLR<2(40.5% vs 67.9%, p=0.005). In a multivariateCox model, NLR≥2(HR: 2.342, 95%CI: 1.095-5.007, p=0.028), pathological depth of tumor(HR: 3.207, 95%CI: 1.114- 9.233, p=0.031), and an ageove r 60(HR: 2.342, 95%CI: 1.117-6.501, p=0.027)were identified as independent prognostic factors for OS after esophagectomy.

CONCLUSIONS

The preoperative NLR was significantly associated with a poor prognosis in esophageal cancer patients who underwent curative esophagectomy following neoadjuvant chemotherapy.

Implications of SNP weighting on single-step genomic predictions for different reference population sizes

We investigated the importance of SNP weighting in populations with 2,000 to 25,000 genotyped animals. Populations were simulated with two effective sizes (20 or 100) and three numbers of QTL (10, 50 or 500). Pedigree information was available for six generations; phenotypes were recorded for the four middle generations. Animals from the last three generations were genotyped for 45,000 SNP. Single-step genomic BLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) were used to estimate genomic EBV using a genomic relationship matrix (G). The WssGBLUP performed better in small genotyped populations; however, any advantage for WssGBLUP was reduced or eliminated when more animals were genotyped. WssGBLUP had greater resolution for genome-wide association (GWA) as did increasing the number of genotyped animals. For few QTL, accuracy was greater for WssGBLUP than ssGBLUP; however, for many QTL, accuracy was the same for both methods. The largest genotyped set was used to assess the dimensionality of genomic information (number of effective SNP). The number of effective SNP was considerably less in weighted G than in unweighted G. Once the number of independent SNP is well represented in the genotyped population, the impact of SNP weighting becomes less important.

Genomic analysis of cow mortality and milk production using a threshold-linear model

The objective of this study was to investigate the feasibility of genomic evaluation for cow mortality and milk production using a single-step methodology. Genomic relationships between cow mortality and milk production were also analyzed. Data included 883,887 (866,700) first-parity, 733,904 (711,211) second-parity, and 516,256 (492,026) third-parity records on cow mortality (305-d milk yields) of Holsteins from Northeast states in the United States. The pedigree consisted of up to 1,690,481 animals including 34,481 bulls genotyped with 36,951 SNP markers. Analyses were conducted with a bivariate threshold-linear model for each parity separately. Genomic information was incorporated as a genomic relationship matrix in the single-step BLUP. Traditional and genomic estimated breeding values (GEBV) were obtained with Gibbs sampling using fixed variances, whereas reliabilities were calculated from variances of GEBV samples. Genomic EBV were then converted into single nucleotide polymorphism (SNP) marker effects. Those SNP effects were categorized according to values corresponding to 1 to 4 standard deviations. Moving averages and variances of SNP effects were calculated for windows of 30 adjacent SNP, and Manhattan plots were created for SNP variances with the same window size. Using Gibbs sampling, the reliability for genotyped bulls for cow mortality was 28 to 30% in EBV and 70 to 72% in GEBV. The reliability for genotyped bulls for 305-d milk yields was 53 to 65% to 81 to 85% in GEBV. Correlations of SNP effects between mortality and 305-d milk yields within categories were the highest with the largest SNP effects and reached >0.7 at 4 standard deviations. All SNP regions explained less than 0.6% of the genetic variance for both traits, except regions close to the DGAT1 gene, which explained up to 2.5% for cow mortality and 4% for 305-d milk yields. Reliability for GEBV with a moderate number of genotyped animals can be calculated by Gibbs samples. Genomic information can greatly increase the reliability of predictions not only for milk but also for mortality. The existence of a common region on Bos taurus autosome 14 affecting both traits may indicate a major gene with a pleiotropic effect on milk and mortality.

Technical note: Avoiding the direct inversion of the numerator relationship matrix for genotyped animals in single-step genomic best linear unbiased prediction solved with the preconditioned conjugate gradient

This paper evaluates an efficient implementation to multiply the inverse of a numerator relationship matrix for genotyped animals () by a vector (). The computation is required for solving mixed model equations in single-step genomic BLUP (ssGBLUP) with the preconditioned conjugate gradient (PCG). The inverse can be decomposed into sparse matrices that are blocks of the sparse inverse of a numerator relationship matrix () including genotyped animals and their ancestors. The elements of were rapidly calculated with the Henderson's rule and stored as sparse matrices in memory. Implementation of was by a series of sparse matrix-vector multiplications. Diagonal elements of , which were required as preconditioners in PCG, were approximated with a Monte Carlo method using 1,000 samples. The efficient implementation of was compared with explicit inversion of with 3 data sets including about 15,000, 81,000, and 570,000 genotyped animals selected from populations with 213,000, 8.2 million, and 10.7 million pedigree animals, respectively. The explicit inversion required 1.8 GB, 49 GB, and 2,415 GB (estimated) of memory, respectively, and 42 s, 56 min, and 13.5 d (estimated), respectively, for the computations. The efficient implementation required <1 MB, 2.9 GB, and 2.3 GB of memory, respectively, and <1 sec, 3 min, and 5 min, respectively, for setting up. Only <1 sec was required for the multiplication in each PCG iteration for any data sets. When the equations in ssGBLUP are solved with the PCG algorithm, is no longer a limiting factor in the computations.

Modeling response to heat stress in pigs from nucleus and commercial farms in different locations in the United States

The purpose of this study was to analyze the impact of seasonal losses due to heat stress in different environments and genetic group combinations. Data were available for 2 different swine populations: purebred Duroc animals raised in nucleus farms in Texas and North Carolina and crosses of Duroc and F females (Landrace × Large White) raised in commercial farms in Missouri and North Carolina; pedigrees provided links between animals from different states. Traits included BW at harvest age for purebred animals and HCW for crossbred animals. Weather data were collected at airports located close to the farms. Heat stress was quantified by a heat load function, defined by the units of temperature-humidity of temperature-humidity index (THI) greater than a certain threshold for 30 to 70 d before phenotype collection. Heat stress responses were quantified by a linear regression of phenotype on heat load. The greatest coefficient of determination occurred with a length of 30 d before phenotype measurements for all states and genetic groups. In the crossbreed data, THI thresholds were 67 in Missouri and 72 in North Carolina. For pure breeds, heat load had the best fit for THI thresholds greater than 70 in North Carolina, although differences in coefficient of determinations were negligible. On the other hand, no optimal THI threshold existed in Texas. In this study, heat stress had a greater impact in commercial farms than in nucleus farms and the effect of heat stress on weight varied by year and state.

Crossbreed evaluations in single-step genomic best linear unbiased predictor using adjusted realized relationship matrices

Combining purebreed and crossbreed information is beneficial for genetic evaluation of some livestock species. Genetic evaluations can use relationships based on genomic information, relying on allele frequencies that are breed specific. Single-step genomic BLUP (ssGBLUP) does not account for different allele frequencies, which could limit the genetic gain in crossbreed evaluations. In this study, we tested the performance of different breed-specific genomic relationship matrices () in ssGBLUP for crossbreed evaluations; we also tested the importance of genotyping crossbred animals. Genotypes were available for purebreeds (AA and BB) and crossbreeds (F) in simulated and real pig populations. The number of genotyped animals was, on average, 4,315 for the simulated population and 15,798 for the real population. Cross-validation was performed on 1,200 and 3,117 F animals in the simulated and real populations, respectively. Simulated scenarios were under no artificial selection, mass selection, or BLUP selection. Two genomic relationship matrices were constructed based on breed-specific allele frequencies: 1) , a genomic relationship matrix centered by breed-specific allele frequencies, and 2) , a genomic relationship matrix centered and scaled by breed-specific allele frequencies. All (the across-breed genomic relationship matrix), , and were also tuned to account for selective genotyping. Using breed-specific allele frequencies reduced the number of negative relationships between 2 purebreeds, pulling the average closer to 0, as in the pedigree-based relationship matrix. For simulated populations that included mass selection, genomic EBV (GEBV) in F, when using and , were, on average, 10% more accurate than ; however, after tuning to account for selective genotyping, provided the same accuracy as for breed-specific genomic relationship matrices. For the real population, accuracies for litter size in F were 0.62 for , , and , and tuning had no impact on accuracy, except for , which was 1 percentage point less accurate. Accuracy of GEBV for number of stillborns in F1 was 0.5 for all tested genomic relationship matrices with no changes after tuning. We observed that genotyping F increased accuracies of GEBV for the same animals by up to 39% compared with having genotypes for only AA and BB. In crossbreed evaluations, accounting for breed-specific allele frequencies promoted changes in G that were not influential enough to improve accuracy of GEBV. Therefore, the best performance of ssGBLUP for crossbreed evaluations requires genotypes for pure- and crossbreeds and no breed-specific adjustments in the realized relationship matrix.