Hundreds of variants clustered in genomic loci and biological pathways affect human height

Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing

Donkeys are widely distributed labour animals in the world. During the process of the domestication and artificial selection of domestic donkeys, body sizes show significant differences among different breeds of donkeys. Based on the genome resequencing data of 103 Chinese indigenous donkeys from 11 breeds (Biyang, Dezhou, Guangling, Hetian, Jiami, Kulun, Qingyang, Turfan, Tibetan, Xinjiang, and Yunnan), seven Spanish donkeys from two breeds (Zamorano~Leonés and Andalusian), and three wild donkeys, we investigated the population structures of Chinese domestic donkeys with different body sizes. We used F_ST and XP-EHH analyses to explore the selected regions related to body sizes. The results showed that Chinese indigenous donkeys have a closer relationship with African wild donkeys than with Asian wild donkeys. LCORL/NCAPG, FAM184B, TBX3, and IHH were identified as genes with strong signals in analysis of selection signature (F_ST and XP-EHH) in large and small donkeys. The seven identified variants can be served as candidate loci affecting the body size of Chinese donkeys. Five of seven loci were located in intron 9 of FAM184B and were in a haplotype block, and one of the identified variants (Chr03:112664848) located in the CDS region of the LCORL gene was found to cause stop-loss. These candidate genes and variants shed new light on the molecular basis of donkey body size and will facilitate the breeding activities of donkeys.

miR-155-3p: processing by-product or rising star in immunity and cancer?

MicroRNAs (miRNAs) are key players in gene regulation that target specific mRNAs for degradation or translational repression. Each miRNA is synthesized as a miRNA duplex comprising two strands (5p and 3p). However, only one of the two strands becomes active and is selectively incorporated into the RNA-induced silencing complex in a process known as miRNA strand selection. Recently, significant progress has been made in understanding the factors and processes involved in strand selection. Here, we explore the selection and functionality of the miRNA star strand (either 5p or 3p), which is generally present in the cell at low levels compared to its partner strand and, historically, has been thought to possess no biological activity. We also highlight the concepts of miRNA arm switching and miRNA isomerism. Finally, we offer insights into the impact of aberrant strand selection on immunity and cancer. Leading us through this journey is miR-155, a well-established regulator of immunity and cancer, and the increasing evidence that its 3p strand plays a role in these arenas. Interestingly, the miR-155-5p/-3p ratio appears to vary dependent on the timing of the immune response, and the 3p strand seems to play a regulatory role upon its partner 5p strand.

The Relationship between Fluid Milk, Water, and 100% Juice and Health Outcomes among Children and Adolescents

Beverages can provide improved nutrient intake and hydration, but also pose concerns related to overnutrition or contamination for children and adolescents who are in a time of critical growth. This narrative review aims to understand the impact of milk, 100% juice, and water consumption on health-related outcomes in youth. The literature review conducted used PubMed, Web of Science, and CABI global. Forty-five research articles met the quality criteria and were included. Health organization and governmental resources were also reviewed to identify current intake and consumption recommendations. All beverages in this review were associated with a variety of desirable and undesirable findings that spanned over 40 different health outcomes. Most studies that assessed milk lacked clear distinction between milk type (flavored vs. unflavored) or fat percentage, making it difficult to understand the impact of milk consumption. The relationship between milk intake and anthropometric-related outcomes were mixed within and across studies. Water was consistently associated with better hydration, while 100% juice and flavored milk intake was associated with more desirable dietary patterns or nutrients that children are currently not consuming adequate amounts of. The implications of these findings were discussed in the context of the National School Lunch Program (NSLP), while considering the impact of issues such as contaminated water and lactose intolerance. This review suggests that water may be an optimal default beverage option in the NSLP to promote hydration and accommodate beverage preferences for those with lactose intolerance.

A Statistical Explanation of the Dunning-Kruger Effect

An explanation of the Dunning-Kruger effect is provided which does not require any psychological explanation, because it is derived as a statistical artifact. This is achieved by specifying a simple statistical model which explicitly takes the (random) boundary constraints into account. The model fits the data almost perfectly.

JEL Classification

A22; C24; C91; D84; D91; I21.

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

Convergence of case-specific epigenetic alterations identify a confluence of genetic vulnerabilities tied to opioid overdose

Opioid use disorder is a highly heterogeneous disease driven by a variety of genetic and environmental risk factors which have yet to be fully elucidated. Opioid overdose, the most severe outcome of opioid use disorder, remains the leading cause of accidental death in the United States. We interrogated the effects of opioid overdose on the brain using ChIP-seq to quantify patterns of H3K27 acetylation in dorsolateral prefrontal cortical neurons isolated from 51 opioid-overdose cases and 51 accidental death controls. Among opioid cases, we observed global hypoacetylation and identified 388 putative enhancers consistently depleted for H3K27ac. Machine learning on H3K27ac patterns predicted case-control status with high accuracy. We focused on case-specific regulatory alterations, revealing 81,399 hypoacetylation events, uncovering vast inter-patient heterogeneity. We developed a strategy to decode this heterogeneity based on convergence analysis, which leveraged promoter-capture Hi-C to identify five genes over-burdened by alterations in their regulatory network or "plexus": ASTN2, KCNMA1, DUSP4, GABBR2, ENOX1. These convergent loci are enriched for opioid use disorder risk genes and heritability for generalized anxiety, number of sexual partners, and years of education. Overall, our multi-pronged approach uncovers neurobiological aspects of opioid use disorder and captures genetic and environmental factors perpetuating the opioid epidemic.

Clinical Profiles and Genetic Spectra of 814 Chinese Children With Short Stature

CONTEXT

Data and studies based on exome sequencing for the genetic evaluation of short stature are limited, and more large-scale studies are warranted. Some factors increase the likelihood of a monogenic cause of short stature, including skeletal dysplasia, severe short stature, and small for gestational age (SGA) without catch-up growth. However, whether these factors can serve as predictors of molecular diagnosis remains unknown.

OBJECTIVE

We aimed to explore the diagnostic efficiency of the associated risk factors and their exome sequences for screening.

METHODS

We defined and applied factors that increased the likelihood of monogenic causes of short stature in diagnostic genetic tests based on next-generation sequencing (NGS) in 814 patients with short stature and at least 1 other factor.

RESULTS

Pathogenic/likely pathogenic (P/LP) variants in genes, copy number variations, and chromosomal abnormalities were identified in 361 patients. We found P/LP variants among 111 genes, and RASopathies comprised the most important etiology. Short stature combined with other phenotypes significantly increased the likelihood of a monogenic cause, including skeletal dysplasia, facial dysmorphism, and intellectual disability, compared with simple severe short stature (<-3 SD scores). We report novel candidate pathogenic genes, KMT2C for unequivocal growth hormone insensitivity and GATA6 for SGA.

CONCLUSION

Our study identified the diagnostic characteristics of NGS in short stature with different risk factors. Our study provides novel insights into the current understanding of the etiology of short stature in patients with different phenotypes.

Partitioning gene-mediated disease heritability without eQTLs

Unknown SNP-to-gene regulatory architecture complicates efforts to link noncoding GWAS associations with genes implicated by sequencing or functional studies. eQTLs are often used to link SNPs to genes, but expression in bulk tissue explains a small fraction of disease heritability. A simple but successful approach has been to link SNPs with nearby genes via base pair windows, but genes may often be regulated by SNPs outside their window. We propose the abstract mediation model (AMM) to estimate (1) the fraction of heritability mediated by the closest or kth-closest gene to each SNP and (2) the mediated heritability enrichment of a gene set (e.g., genes with rare-variant associations). AMM jointly estimates these quantities by matching the decay in SNP enrichment with distance from genes in the gene set. Across 47 complex traits and diseases, we estimate that the closest gene to each SNP mediates 27% (SE: 6%) of heritability and that a substantial fraction is mediated by genes outside the ten closest. Mendelian disease genes are strongly enriched for common-variant heritability; for example, just 21 dyslipidemia genes mediate 25% of LDL heritability (211× enrichment, p = 0.01). Among brain-related traits, genes involved in neurodevelopmental disorders are only about 4× enriched, but gene expression patterns are highly informative, as they have detectable differences in per-gene heritability even among weakly brain-expressed genes.

Analysis of rare genetic variation underlying cardiometabolic diseases and traits among 200,000 individuals in the UK Biobank

Cardiometabolic diseases are the leading cause of death worldwide. Despite a known genetic component, our understanding of these diseases remains incomplete. Here, we analyzed the contribution of rare variants to 57 diseases and 26 cardiometabolic traits, using data from 200,337 UK Biobank participants with whole-exome sequencing. We identified 57 gene-based associations, with broad replication of novel signals in Geisinger MyCode. There was a striking risk associated with mutations in known Mendelian disease genes, including MYBPC3, LDLR, GCK, PKD1 and TTN. Many genes showed independent convergence of rare and common variant evidence, including an association between GIGYF1 and type 2 diabetes. We identified several large effect associations for height and 18 unique genes associated with blood lipid or glucose levels. Finally, we found that between 1.0% and 2.4% of participants carried rare potentially pathogenic variants for cardiometabolic disorders. These findings may facilitate studies aimed at therapeutics and screening of these common disorders.

Early anthropometric indicators of type 2 diabetes mellitus

PURPOSE OF REVIEW

With the rapidly increasing incidence of type 2 diabetes mellitus (T2DM) in youth (as in adults), it is critical to recognize phenotypic markers that can help predict and potentially prevent its onset, and reduce the associated burden of the disease for patients, families, and society. In this review, we summarize the most recent literature characterizing growth, puberty, and body composition in youth at risk for or who have T2DM.

RECENT FINDINGS

There is an inverse, nonlinear relationship between birth weight and future risk of developing T2DM. Height seems to have an inverse correlation with risk for diabetes. Earlier onset of puberty in males and females is associated with the T2DM phenotype. While adiposity is a known correlate of T2DM, visceral adiposity as represented by waist circumference has emerged as one of the key determinants of T2DM in population-based studies globally. Thresholds for body mass index vary across ethnicities in predicting risk for T2DM, depending on genetic factors and fat-distribution profiles.

SUMMARY

Emerging links between T2DM and dysregulated parameters of growth and development highlight the importance of early recognition of modifiable risk factors and the creation of individualized screening protocols.

VIDEO ABSTRACT

http://links.lww.com/COE/A31.

Detection of selection signatures in South African Mutton Merino sheep using whole-genome sequencing data

The South African Mutton Merino (SAMM), a dual-purpose (meat and wool) sheep breed, is characterized by its excellent performance on growth, carcass traits and meat quality compared to other fine-wool Merino breeds. Nowadays, the SAMM breed has been widely used to cross with commercial and indigenous fine-wool or coarse-wool breeds to improve the growth and meat performance in many countries. To date, however, little is known about the genetic basis for its prominent characteristics. In this study, whole-genome sequences of 10 SAMM were sequenced and the selection signatures were analyzed together with those of 39 Australian Merino and Chinese Merino (wool-type Merino) by F_ST , iHS, and XP-EHH methods. In total, 313 genes in 277 regions were identified by at least 2 methods with the signal of selection and 21 of them were identified by all three methods. We highlighted a list of interesting genes, including GHR, LCORL, SMO, NCAPG, DCC, IBSP, PPARGC1A, PACRGL, PRDM5, XYLB, AHCYL2, TEFM, AFG1L, and FAM184B, which have been shown to be involved in growth, carcass traits, and meat quality by previous studies. Herein, GHR, encoding a transmembrane receptor for growth hormone, is the most notable one. We report the first study on selection signatures analysis of SAMM at whole-genome sequence level. These results provide new insights into the genetic mechanisms underlying the growth and carcass traits in SAMM.

Identification of the genetic mechanism that associates L3MBTL3 to multiple sclerosis

Multiple sclerosis (MS) is a complex and demyelinating disease of the central nervous system. One of the challenges of the post-GWAS era is to understand the molecular basis of statistical associations to reveal gene networks and potential therapeutic targets. The L3MBTL3 locus has been associated with MS risk by GWAS. To identify the causal variant of the locus, we performed fine mapping in a cohort of 3440 MS patients and 1688 healthy controls. The variant that best explained the association was rs6569648 (P = 4.13E-10, OR = 0.71, 95% CI = 0.64-0.79), which tagged rs7740107, located in intron 7 of L3MBTL3. The rs7740107 (A/T) variant has been reported to be the best expression and splice quantitative trait locus (eQTL and sQTL) of the region in up to 35 human GTEx tissues. By sequencing RNA from blood of 17 MS patients and quantification by digital qPCR, we determined that this eQTL/sQTL originated from the expression of a novel short transcript starting in intron 7 near rs7740107. The short transcript was translated into three proteins starting at different translation initiation codons. These N-terminal truncated proteins lacked the region where L3MBTL3 interacts with the transcriptional regulator RBPJ (Recombination Signal Binding Protein for Immunoglobulin Kappa J Region) which, in turn, regulates the Notch signaling pathway. Our data and other functional studies suggest that the genetic mechanism underlying the MS association of rs7740107 affects not only the expression of L3MBTL3 isoforms, but might also involve the Notch signaling pathway.

Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals

Human leukocyte antigen (HLA) gene variants in the major histocompatibility complex (MHC) region are associated with numerous complex human diseases and quantitative traits. Previous phenome-wide association studies (PheWAS) for this region demonstrated that HLA association patterns to the phenome have both population-specific and population-shared components. We performed MHC PheWAS in the Korean population by analyzing associations between phenotypes and genetic variants in the MHC region using the Korea Biobank Array project data samples from the Korean Genome and Epidemiology Study (KoGES) cohorts. Using this single-population dataset, we curated and analyzed 82 phenotypes for 125 673 Korean individuals after imputing HLA using CookHLA, a recently developed imputation framework. More than one-third of these phenotypes showed significant associations, confirming 56 known associations and discovering 13 novel association signals that were not reported previously. In addition, we analyzed heritability explained by the variants in the MHC region and genetic correlations among phenotypes based on the MHC variants.

Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses

Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorphisms (SNPs), analysis of the genomic relationship revealed substructures reflecting breed origin and different breeding goals of the contributing breeding associations. A genome-wide association study confirmed a known quantitative trait locus (QTL) for withers height on equine chromosome (ECA) 3 close to LCORL and identified a further significant peak on ECA 1. Using a single-step approach with a combined relationship matrix, the estimated heritability for withers height was 0.31 (SE = 0.08) and the corresponding genomic breeding values ranged from − 2.94 to 2.96 cm. A mean reliability of 0.38 was realized for these breeding values. The analyses of withers height showed that compiling a reference population across breeds is a suitable strategy for German Warmblood horses. The single-step method is an appealing approach for practical genomic prediction in horses, because not many genotypes are available yet and animals without genotypes can by this way directly contribute to the estimation system.

Predicting Physical Appearance from DNA Data-Towards Genomic Solutions

The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.

A data-adaptive Bayesian regression approach for polygenic risk prediction

MOTIVATION

Polygenic risk score (PRS) has been widely exploited for genetic risk prediction due to its accuracy and conceptual simplicity. We introduce a unified Bayesian regression framework, NeuPred, for PRS construction, which accommodates varying genetic architectures and improves overall prediction accuracy for complex diseases by allowing for a wide class of prior choices. To take full advantage of the framework, we propose a summary-statistics-based cross-validation strategy to automatically select suitable chromosome-level priors, which demonstrates a striking variability of the prior preference of each chromosome, for the same complex disease, and further significantly improves the prediction accuracy.

RESULTS

Simulation studies and real data applications with seven disease datasets from the Wellcome Trust Case Control Consortium cohort and eight groups of large-scale genome-wide association studies demonstrate that NeuPred achieves substantial and consistent improvements in terms of predictive r2 over existing methods. In addition, NeuPred has similar or advantageous computational efficiency compared with the state-of-the-art Bayesian methods.

AVAILABILITY AND IMPLEMENTATION

The R package implementing NeuPred is available at https://github.com/shuangsong0110/NeuPred.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Polymorphisms in the mTOR-PI3K-Akt pathway, energy balance-related exposures and colorectal cancer risk in the Netherlands Cohort Study

BACKGROUND

The mTOR-PI3K-Akt pathway influences cell metabolism and (malignant) cell growth. We generated sex-specific polygenic risk scores capturing natural variation in 7 out of 10 top-ranked genes in this pathway. We studied the scores directly and in interaction with energy balance-related factors (body mass index (BMI), trouser/skirt size, height, physical activity, and early life energy restriction) in relation to colorectal cancer (CRC) risk in the Netherlands Cohort Study (NLCS) (n=120,852). The NLCS has a case-cohort design and 20.3 years of follow-up. Participants completed a baseline questionnaire on diet and cancer in 1986 when 55-69 years old. ~75% of the cohort returned toenail clippings used for DNA isolation and genotyping (n subcohort=3,793, n cases=3,464). To generate the scores, the dataset was split in two and risk alleles were defined and weighted based on sex-specific associations with CRC risk in the other dataset half, because there were no SNPs in the top-ranked genes associated with CRC risk in previous genome-wide association studies at a significance level p<1*10^-5.

RESULTS

Cox regression analyses showed positive associations between the sex-specific polygenic risk scores and colon but not rectal cancer risk in men and women, with hazard ratios for continuously modeled scores close to 1.10. There was no modifying effect observed of the scores on associations between the energy balance-related factors and CRC risk. However, BMI (in men), non-occupational physical activity (in women), and height (in men and women) were associated with the risk of CRC, in particular (proximal and distal) colon cancer, in the direction as expected in the lower tertiles of the sex-specific polygenic risk scores.

CONCLUSIONS

Current data suggest that the mTOR-PI3K-Akt pathway may be involved in colon cancer development. This study thereby sheds more light on colon cancer etiology through use of genetic variation in the mTOR-PI3K-Akt pathway.

SNP and Haplotype Regional Heritability Mapping (SNHap-RHM): Joint Mapping of Common and Rare Variation Affecting Complex Traits

We describe a genome-wide analytical approach, SNP and Haplotype Regional Heritability Mapping (SNHap-RHM), that provides regional estimates of the heritability across locally defined regions in the genome. This approach utilises relationship matrices that are based on sharing of SNP and haplotype alleles at local haplotype blocks delimited by recombination boundaries in the genome. We implemented the approach on simulated data and show that the haplotype-based regional GRMs capture variation that is complementary to that captured by SNP-based regional GRMs, and thus justifying the fitting of the two GRMs jointly in a single analysis (SNHap-RHM). SNHap-RHM captures regions in the genome contributing to the phenotypic variation that existing genome-wide analysis methods may fail to capture. We further demonstrate that there are real benefits to be gained from this approach by applying it to real data from about 20,000 individuals from the Generation Scotland: Scottish Family Health Study. We analysed height and major depressive disorder (MDD). We identified seven genomic regions that are genome-wide significant for height, and three regions significant at a suggestive threshold (p-value < 1 × 10-5) for MDD. These significant regions have genes mapped to within 400 kb of them. The genes mapped for height have been reported to be associated with height in humans. Similarly, those mapped for MDD have been reported to be associated with major depressive disorder and other psychiatry phenotypes. The results show that SNHap-RHM presents an exciting new opportunity to analyse complex traits by allowing the joint mapping of novel genomic regions tagged by either SNPs or haplotypes, potentially leading to the recovery of some of the "missing" heritability.

A Novel Osteochondrodysplasia With Empty Sella Associates With a TBX2 Variant

Skeletal dysplasias comprise a heterogenous group of developmental disorders of skeletal and cartilaginous tissues. Several different forms have been described and the full spectrum of their clinical manifestations and underlying genetic causes are still incompletely understood. We report a three-generation Finnish family with an unusual, autosomal dominant form of osteochondrodysplasia and an empty sella. Affected individuals (age range 24-44 years) exhibit unusual codfish-shaped vertebrae, severe early-onset and debilitating osteoarthritis and an empty sella without endocrine abnormalities. Clinical characteristics also include mild dysmorphic features, reduced sitting height ratio, and obesity. Whole-exome sequencing excluded known skeletal dysplasias and identified a novel heterozygous missense mutation c.899C>T (p.Thr300Met) in TBX2, confirmed by Sanger sequencing. TBX2 is important for development of the skeleton and the brain and three prior reports have described variations in TBX2 in patients portraying a complex phenotype with vertebral anomalies, craniofacial dysmorphism and endocrine dysfunctions. Our mutation lies near a previously reported disease-causing variant and is predicted pathogenic with deleterious effects on protein function. Our findings expand the current spectrum of skeletal dysplasias, support the association of TBX2 mutations with skeletal dysplasia and suggest a role for TBX2 in development of the spinal and craniofacial structures and the pituitary gland.

Dynamic Changes in Serum IGF-I and Growth During Infancy: Associations to Body Fat, Target Height, and PAPPA2 Genotype

CONTEXT

IGF-I is important for postnatal growth and may be of diagnostic value in infants suspected of pituitary disease; however, little is known about the impact of IGF-I and its determinants on infant growth. Importantly, detailed reference ranges for IGF-I and IGF binding protein-3 (IGFBP-3) concentrations during infancy are lacking.

OBJECTIVE

To evaluate the rapid changes in weight and length as well as their determinants in healthy infants, and to establish age- and sex-specific reference curves for IGF-I and IGFBP-3 in children aged 0 to 1 years.

DESIGN

Prospective longitudinal study.

SETTING

Cohort study.

PARTICIPANTS

A total of 233 healthy children (114 girls) with repeated blood samples during the first year of life.

MAIN OUTCOME MEASURE(S)

Serum concentrations of IGF-I and IGFBP-3, length velocity, weight velocity, and PAPPA2 (rs1325598) genotype.

RESULTS

Individual trajectories of length and weight velocities were sex specific. We provide detailed reference curves based on longitudinal data for IGF-I and IGFBP-3 during infancy. In both girls and boys, IGF-I decreased during infancy, whereas IGFBP-3 remained stable. IGF-I and IGFBP-3, but not PAPPA2 genotype, were positively associated with weight gain, but not with longitudinal growth. When stratified by sex, the association between weight gain and IGF-I only remained significant in girls.

CONCLUSIONS

Interestingly, we found a significant association between IGF-I and infant weight gain in girls, but not with longitudinal growth in the first year of life. Our findings highlight the role of IGF-I as an important anabolic hormone that is not limited to linear growth.

Gene Set Enrichment Analsyes Identify Pathways Involved in Genetic Risk for Diabetic Retinopathy

To identify functionally related genes associated with diabetic retinopathy (DR) risk using gene set enrichment analyses applied to genome-wide association study meta-analyses.

METHODS

We analyzed DR GWAS meta-analyses performed on 3246 Europeans and 2611 African Americans with type 2 diabetes. Gene sets relevant to 5 key DR pathophysiology processes were investigated: tissue injury, vascular events, metabolic events and glial dysregulation, neuronal dysfunction, and inflammation. Keywords relevant to these processes were queried in 4 pathway and ontology databases. Two GSEA methods, Meta-Analysis Gene set Enrichment of variaNT Associations (MAGENTA) and Multi-marker Analysis of GenoMic Annotation (MAGMA), were used. Gene sets were defined to be enriched for gene associations with DR if the P value corrected for multiple testing (Pcorr) was <.05.

RESULTS

Five gene sets were significantly enriched for numerous modest genetic associations with DR in one method (MAGENTA or MAGMA) and also at least nominally significant (uncorrected P < .05) in the other method. These pathways were regulation of the lipid catabolic process (2-fold enrichment, Pcorr = .014); nitric oxide biosynthesis (1.92-fold enrichment, Pcorr = .022); lipid digestion, mobilization, and transport (1.6-fold enrichment, P = .032); apoptosis (1.53-fold enrichment, P = .041); and retinal ganglion cell degeneration (2-fold enrichment, Pcorr = .049). The interferon gamma (IFNG) gene, previously implicated in DR by protein-protein interactions in our GWAS, was among the top ranked genes in the nitric oxide pathway (best variant P = .0001).

CONCLUSIONS

These GSEA indicate that variants in genes involved in oxidative stress, lipid transport and catabolism, and cell degeneration are enriched for genes associated with DR risk. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.

A Genetic Map of the Modern Urban Society of Amsterdam

Genetic differences between individuals underlie susceptibility to many diseases. Genome-wide association studies (GWAS) have discovered many susceptibility genes but were often limited to cohorts of predominantly European ancestry. Genetic diversity between individuals due to different ancestries and evolutionary histories shows that this approach has limitations. In order to gain a better understanding of the associated genetic variation, we need a more global genomics approach including a greater diversity. Here, we introduce the Healthy Life in an Urban Setting (HELIUS) cohort. The HELIUS cohort consists of participants living in Amsterdam, with a level of diversity that reflects the Dutch colonial and recent migration past. The current study includes 10,283 participants with genetic data available from seven groups of inhabitants, namely, Dutch, African Surinamese, South-Asian Surinamese, Turkish, Moroccan, Ghanaian, and Javanese Surinamese. First, we describe the genetic variation and admixture within the HELIUS cohort. Second, we show the challenges during imputation when having a genetically diverse cohort. Third, we conduct a body mass index (BMI) and height GWAS where we investigate the effects of a joint analysis of the entire cohort and a meta-analysis approach for the different subgroups. Finally, we construct polygenic scores for BMI and height and compare their predictive power across the different ethnic groups. Overall, we give a comprehensive overview of a genetically diverse cohort from Amsterdam. Our study emphasizes the importance of a less biased and more realistic representation of urban populations for mapping genetic associations with complex traits and disease risk for all.

Estimating prevalence of human traits among populations from polygenic risk scores

The genetic basis of phenotypic variation across populations has not been well explained for most traits. Several factors may cause disparities, from variation in environments to divergent population genetic structure. We hypothesized that a population-level polygenic risk score (PRS) can explain phenotypic variation among geographic populations based solely on risk allele frequencies. We applied a population-specific PRS (psPRS) to 26 populations from the 1000 Genomes to four phenotypes: lactase persistence (LP), melanoma, multiple sclerosis (MS) and height. Our models assumed additive genetic architecture among the polymorphisms in the psPRSs, as is convention. Linear psPRSs explained a significant proportion of trait variance ranging from 0.32 for height in men to 0.88 for melanoma. The best models for LP and height were linear, while those for melanoma and MS were nonlinear. As not all variants in a PRS may confer similar, or even any, risk among diverse populations, we also filtered out SNPs to assess whether variance explained was improved using psPRSs with fewer SNPs. Variance explained usually improved with fewer SNPs in the psPRS and was as high as 0.99 for height in men using only 548 of the initial 4208 SNPs. That reducing SNPs improves psPRSs performance may indicate that missing heritability is partially due to complex architecture that does not mandate additivity, undiscovered variants or spurious associations in the databases. We demonstrated that PRS-based analyses can be used across diverse populations and phenotypes for population prediction and that these comparisons can identify the universal risk variants.

The Prevailing Role of Topoisomerase 2 Beta and its Associated Genes in Neurons

Topoisomerase 2 beta (TOP2β) is an enzyme that alters the topological states of DNA by making a transient double-strand break during the transcription process. The direct interaction of TOP2β with DNA strand results in transcriptional regulation of certain genes and some studies have suggested that a particular set of genes are regulated by TOP2β, which have a prominent role in various stages of neuron from development to degeneration. In this review, we discuss the role of TOP2β in various phases of the neuron's life. Based on the existing reports, we have compiled the list of genes, which are directly regulated by the enzyme, from different studies and performed their functional classification. We discuss the role of these genes in neurogenesis, neuron migration, fate determination, differentiation and maturation, generation of neural circuits, and senescence.

Functional convalescent plasma antibodies and pre-infusion titers shape the early severe COVID-19 immune response

Transfer of convalescent plasma (CP) had been proposed early during the SARS-CoV-2 pandemic as an accessible therapy, yet trial results worldwide have been mixed, potentially due to the heterogeneous nature of CP. Here we perform deep profiling of SARS-CoV-2-specific antibody titer, Fc-receptor binding, and Fc-mediated functional assays in CP units, as well as in plasma from hospitalized COVID-19 patients before and after CP administration. The profiling results show that, although all recipients exhibit expanded SARS-CoV-2-specific humoral immune responses, CP units contain more functional antibodies than recipient plasma. Meanwhile, CP functional profiles influence the evolution of recipient humoral immunity in conjuncture with the recipient's pre-existing SARS-CoV2-specific antibody titers: CP-derived SARS-CoV-2 nucleocapsid-specific antibody functions are associated with muted humoral immune evolution in patients with high titer anti-spike IgG. Our data thus provide insights into the unexpected impact of CP-derived functional anti-spike and anti-nucleocapsid antibodies on the evolution of SARS-CoV-2-specific response following severe infection.

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag" variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit genetic data sharing with an untrusted imputation service. Here, we developed secure genotype imputation using efficient homomorphic encryption (HE) techniques. In HE-based methods, the genotype data are secure while it is in transit, at rest, and in analysis. It can only be decrypted by the owner. We compared secure imputation with three state-of-the-art non-secure methods and found that HE-based methods provide genetic data security with comparable accuracy for common variants. HE-based methods have time and memory requirements that are comparable or lower than those for the non-secure methods. Our results provide evidence that HE-based methods can practically perform resource-intensive computations for high-throughput genetic data analysis. The source code is freely available for download at https://github.com/K-miran/secure-imputation.

Bench Research Informed by GWAS Results

Scientifically interesting as well as practically important phenotypes often belong to the realm of complex traits. To the extent that these traits are hereditary, they are usually 'highly polygenic'. The study of such traits presents a challenge for researchers, as the complex genetic architecture of such traits makes it nearly impossible to utilise many of the usual methods of reverse genetics, which often focus on specific genes. In recent years, thousands of genome-wide association studies (GWAS) were undertaken to explore the relationships between complex traits and a large number of genetic factors, most of which are characterised by tiny effects. In this review, we aim to familiarise 'wet biologists' with approaches for the interpretation of GWAS results, to clarify some issues that may seem counterintuitive and to assess the possibility of using GWAS results in experiments on various complex traits.

Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis

As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Human selection and targeted breeding have produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that help us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with enrichment analysis on 757 dogs using 118,879 SNPs. The genomic heritability (h²) was 0.33 for height and 0.28 for weight trait in Jindo. At p-value < 5 × 10^-5, ten, six, thirteen and eleven SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our results, HHIP, LCORL and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR and PTPN2, IGFI and RASAL2 for weight can be the potential candidate genes because of the significant SNPs located in their intronic or upstream regions. The gene-set enrichment analysis highlighted here nine and seven overlapping significant (p < 0.05) gene ontology (GO) terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signalling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding of the Jindo dog's population.

Polygenic Score for Smoking is associated with Externalizing Psychopathology and Disinhibited Personality Traits but not Internalizing Psychopathology in Adolescence

We examined whether a polygenic score (PGS) for smoking measured genetic risk for general behavioral disinhibition by estimating its associations with externalizing and internalizing psychopathology and related personality traits at multiple time points in adolescence (ages 11, 14, and 17 years; N = 3225). The smoking PGS had strong associations with the stable variance across time for all the externalizing measures (mean standardized β = .27), agreeableness (β = -.22, 95% CI: -.28, -.16), and conscientiousness (β = -.19, 95% CI: -.24, -.13), but was not significantly associated with internalizing measures (mean β = .06) or extraversion (β = .01, 95% CI: -.05, .07). After controlling for smoking at age 17, the associations with externalizing, low agreeableness, and low conscientiousness remained statistically significant. The smoking PGS measures genetic influences that contribute to a spectrum of phenotypes related to behavioral disinhibition including externalizing psychopathology and normal-range personality traits related to behavioral control, but not internalizing psychopathology.

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMI_CL, BMI_BL, and BMI_BH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMI_CL, and BMI_BL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.

The genetic basis of spatial cognitive variation in a food-caching bird

Spatial cognition is used by most organisms to navigate their environment. Some species rely particularly heavily on specialized spatial cognition to survive, suggesting that a heritable component of cognition may be under natural selection. This idea remains largely untested outside of humans, perhaps because cognition in general is known to be strongly affected by learning and experience.^1-4 We investigated the genetic basis of individual variation in spatial cognition used by non-migratory food-caching birds to recover food stores and survive harsh montane winters. Comparing the genomes of wild, free-living birds ranging from best to worst in their performance on a spatial cognitive task revealed significant associations with genes involved in neuron growth and development and hippocampal function. These results identify candidate genes associated with differences in spatial cognition and provide a critical link connecting individual variation in spatial cognition with natural selection.

Positive association between actinic keratosis and internal malignancies: a nationwide population-based cohort study

Little is known about the comorbidities in actinic keratosis patients. To evaluate the association of actinic keratosis with certain malignancies. All patients with actinic keratosis (n = 61,438) and age- and sex-matched control subjects (n = 307,190) at a 5:1 ratio were enrolled using data from the Korean National Health Insurance Service between the years 2007 and 2014. In subjects with actinic keratosis, overall cancer incidence was higher than that for controls after income level, habitat, diabetes, hypertension, and dyslipidemia were adjusted (Hazard Ratio [HR] = 1.43 [95% confidence interval 1.38–1.47]). The positive association of specific cancers were observed in the following order: skin cancer (HR = 3.43 [2.47–4.75]), oral cavity and pharyngeal cancer (HR = 1.99 [1.57–2.52]), lymphoma (HR = 1.59 [1.28–1.96]), leukemia (HR = 1.35 [1.03–1.77]), prostate cancer (HR = 1.35 [1.21–1.51]), renal cancer (HR = 1.29 [1.02–1.63]), liver cancer (HR = 1.21 [1.09–1.35]), thyroid cancer (HR = 1.20 [1.05–1.38]), and gastric cancer (HR = 1.13 [1.03–1.23]). Although further research on pathologic mechanism is needed, the implications of a positive correlation between actinic keratosis and internal organ malignancies has great significance.

Evolution of Lactase Persistence: Turbo-Charging Adaptation in Growth Under the Selective Pressure of Maternal Mortality?

The emergence of the capacity to digest milk in some populations represents a landmark in human evolution, linking genetic change with a component of niche construction, namely dairying. Alleles promoting continued activity of the enzyme lactase through the life-course (lactase persistence) evolved in several global regions within the last 7,000 years. In some European regions, these alleles underwent rapid selection and must have profoundly affected fertility or mortality. Elsewhere, alleles spread more locally. However, the functional benefits underlying the rapid spread of lactase persistence remain unclear. Here, we set out the hypothesis that lactase persistence promoted skeletal growth, thereby offering a generic rapid solution to childbirth complications arising from exposure to ecological change, or to new environments through migration. Since reduced maternal growth and greater neonatal size both increase the risk of obstructed labour, any ecological exposure impacting these traits may increase maternal mortality risk. Over many generations, maternal skeletal dimensions could adapt to new ecological conditions through genetic change. However, this adaptive strategy would fail if ecological change was rapid, including through migration into new niches. We propose that the combination of consuming milk and lactase persistence could have reduced maternal mortality by promoting growth of the pelvis after weaning, while high calcium intake would reduce risk of pelvic deformities. Our conceptual framework provides locally relevant hypotheses to explain selection for lactase persistence in different global regions. For any given diet and individual genotype, the combination of lactase persistence and milk consumption would divert more energy to skeletal growth, either increasing pelvic dimensions or buffering them from worsening ecological conditions. The emergence of lactase persistence among dairying populations could have helped early European farmers adapt rapidly to northern latitudes, East African pastoralists adapt to sudden climate shifts to drier environments, and Near Eastern populations counteract secular declines in height associated with early agriculture. In each case, we assume that lactase persistence accelerated the timescale over which maternal skeletal dimensions could change, thus promoting both maternal and offspring survival. Where lactase persistence did not emerge, birth weight was constrained at lower levels, and this contributes to contemporary variability in diabetes risk.

A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens

BACKGROUND

Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a "large" number of genes with "small" effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size.

METHODS

The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring significant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring significant SNPs (1 Mb up/downstream) and the combined regions harbouring non-significant SNPs.

RESULTS

GWAS revealed 25 genomic regions harbouring 96 significant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67-66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained ~ 30% of the total genetic variance. The region harbouring significant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (~ 65.67-66.31 Mb).

CONCLUSIONS

To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identified regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-significant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.

Pearl lecture: Biological normalcy: A new framework for biocultural analysis of human population variation

Biological normalcy is a new analytical framework for understanding the bi-directional relationships between the biology of populations and cultural norms. Populations are characterized by statistical distributions-that is, measures of central tendency and variance-for biological traits, and these co-exist in societies with ideas about what constitutes "normal" human bodies, that is, normative views about what bodies "should" be like. While statistical norms may carry no explicit evaluative weight, the question is how they are related to judgments about what is "normal" or "abnormal." In a 1947 paper, Margaret Mead recognized their potential relationship: "normal…may refer to the statistically usual in the culture-usually without any recognition that this is culturally relative-so that the statistically usual is identified with the basically human…." Despite her observations over 70 years ago, little has been done on this topic, yet such work promises new insights into the relationship between culture and biology, here described at the population level, rather than as individual genetic characteristics. Using examples of sex/gender, race/ethnicity, age, and my work on human variation in the ability to drink milk, I outline the ways in which statistical norms may: influence individuals' perceptions of what is "normal" (Mead's "basically human"); lead to normative judgments about what human biology "should" be ("ethno-biocentrism") that are reinforced by biases in discourse about human variation; and potentially feedback to mold the biological characteristics of a population.

Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders

Common genetic variation appears to largely influence risk for neuropsychiatric disorders through effects on gene regulation. It is therefore possible to shed light on the biology of these conditions by testing for enrichment of associated genetic variation within regulatory genomic regions operating in specific tissues or cell types. Here, we have used the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) to map open chromatin (an index of active regulatory genomic regions) in bulk tissue, NeuN+ and NeuN- nuclei from the prenatal human frontal cortex, and tested enrichment of single-nucleotide polymorphism (SNP) heritability for five neuropsychiatric disorders (autism spectrum disorder, attention deficit hyperactivity disorder [ADHD], bipolar disorder, major depressive disorder, and schizophrenia) within these regions. We observed significant enrichment of SNP heritability for ADHD, major depressive disorder, and schizophrenia within open chromatin regions (OCRs) mapped in bulk fetal frontal cortex, and for all five tested neuropsychiatric conditions when we restricted these sites to those overlapping histone modifications indicative of enhancers (H3K4me1) or promoters (H3K4me3) in fetal brain. SNP heritability for neuropsychiatric disorders was significantly enriched in OCRs identified in fetal frontal cortex NeuN- as well as NeuN+ nuclei overlapping fetal brain H3K4me1 or H3K4me3 sites. We additionally demonstrate the utility of our mapped OCRs for prioritizing potentially functional SNPs at genome-wide significant risk loci for neuropsychiatric disorders. Our data provide evidence for an early neurodevelopmental component to a range of neuropsychiatric conditions and highlight an important role for regulatory genomic regions active within both NeuN+ and NeuN- cells of the prenatal brain.

Short Stature: Understanding the Stature of Ethnicity in Height Determination

Height is a polygenic trait with a high degree of heritability. Most (95%) children with short stature (defined as height below the third percentile) and poor growth (growth velocity <5 cm/year) do not have an endocrine disorder. The genetic basis for stature potential has been evaluated in recent years and is increasingly being recognized as a major basis for variation in height between different ethnic populations. Numerous genome-wide association studies have identified hundreds of loci linked to human growth. Apart from the genetic factors, various environmental, nutritional, hormonal, and socioeconomic factors also influence the height, and stature of individuals varies between different geographical locations and ethnic groups. Ethnically different populations might respond differently to the same environmental factors and thus the final height in different ethnic groups is different. This review covers in detail the short stature of African Pygmies and Andamanese Islanders along with the possible causative factors responsible for the variation in height in these ethnic groups.

Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences

Late-onset Alzheimer's disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.

Gene polymorphisms in leptin and its receptor and the response to growth hormone treatment in patients with idiopathic growth hormone deficiency

This study aimed to investigate the relationships between genetic polymorphisms of leptin/receptor genes and clinical/biochemical characteristics in children with growth hormone deficiency (GHD). Ninety-three GHD children and 69 age-matched normal controls were enrolled. Anthropometric measurements, bone age, and laboratory test results were obtained. Polymorphisms in the LEP gene promoter locus (LEP-2548, rs7799039) and LEPR genes (K109R, rs1137100 and Q223R, rs1137101) were analyzed using PCR-RFLP. The serum leptin levels were measured using an ELISA kit. The median height and BMI z-scores of all GHD subjects were -2.20 and -0.26, respectively, and those of normal controls were -0.30 and -0.13, respectively. The serum leptin levels were similar between GHD subjects and normal controls (p = 0.537), but those were different between the complete GHD (6.97 ng/mL) and partial GHD (4.22 ng/mL) groups (p = 0.047). There were no differences in the genotypic distributions of LEP-2548, LEPR K109R, and Q223R between GHD subjects and normal controls. However, GHD subjects with the G allele at LEP-2548 showed higher IGF-1 (p = 0.047) and IGFBP-3 SDSs (p = 0.027) than GHD subjects with the A allele. GHD subjects with the G allele at LEPR Q223R showed lower stimulated GH levels (p = 0.023) and greater height gain after 1 year of GH treatment (p = 0.034) than GHD subjects with the A allele. In conclusion, leptin/leptin receptor genes are suggested to have the role of growth-related factors, which can affect various growth responses in children who share the same disease entity.

Reliability of phenotype estimation and extended classification of ancestry using decedent samples

The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both markers have been validated for use in forensic biology, there is little data to determine the practical utility of these estimations to assist in identifying missing persons using decedent casework samples. The accuracy and utility of phenotypic and ancestral estimations were investigated for 300 samples received by the Los Angeles County Department of Medical Examiner-Coroner. piSNP genotypes were translated into hair and eye colors using the Forenseq™ Universal Analysis Software (UAS) on the MiSeq FGx™ and the HIrisPlex System, and statistical accuracy was evaluated in context with the reported decedent characteristics. Similarly, estimates of each decedent's biogeographical ancestry were compared to assess the efficacy of these markers to predict ancestry correctly. The average UAS and the HIrisPlex system prediction accuracy for brown and blue eyes were 95.3% and 96.2%, respectively. Intermediate eye color could not be predicted with high accuracy using either system. Other than the black hair phenotype reporting an accuracy that exceeded 90% using either system, hair color was also too variable to be predicted with high accuracy. The FROG-kb database distinguishes decedents adequately beyond the Asian, African, European, and Admixed American global ancestries provided by the MiSeq FGx™ UAS PCA plots. FROG-kb correctly identified Middle Eastern, Pacific Islander, Latin American, or Jewish ancestries with accuracies of 70.0%, 81.8%, 73.8%, and 86.7%, respectively.

Contribution of Ghrelin to the Pathogenesis of Growth Hormone Deficiency

In this review we described the interactions between ghrelin and the growth hormone (GH)-insulin-like growth factor 1 (IGF-1) axis in children and adults with growth hormone deficiency (GHD). A possible involvement of these interactions in the pathogenesis of unexplained cases of GHD was suggested. Current research provides more and more details to the knowledge on the circadian rhythm of ghrelin. We gathered reports on the decreasing effect of Helicobacter pylori-related chronic gastritis on the number of ghrelin immunopositive cells and the consequent decrease in ghrelin serum concentration. The gastrointestinal tract microflora modification of the ghrelin action, by the mechanism of molecular mimicry, was also stressed. Moreover, the mutual relationships between ghrelin and the TSH-FT4/FT3 axis in growth and metabolic processes are described. It is to be recalled that FT4 and FT3 exert a permissive impact on IGF-1 action and, in turn, GH, in reaction mediated by IGF-1, enhances the monodeiodination of FT4 to FT3. Finally, we discussed the latest attempts to use the GH secretagogue receptor (GHS-R) analogues for possible diagnostic and therapeutic purposes.

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.

Dose-response association between adult height and all-cause mortality: a systematic review and meta-analysis of cohort studies

BACKGROUND

We conducted a systematic review and meta-analysis from published cohort studies to examine the association of adult height and all-cause mortality and to further explore the dose-response association.

METHODS

PubMed, The Cochrane Library, The Ovid, CNKI, CQVIP and Wanfang databases were searched for articles published from database inception to 6 February 2018. We used the DerSimonian-Laird random-effects model to estimate the quantitative association between adult height and all-cause mortality and the restricted cubic splines to model the dose-response association.

RESULTS

We included 15 articles, with 1 533 438 death events and 2 854 543 study participants. For each 5-cm height increase below the average, the risk of all-cause mortality was reduced by 7% [relative risk (RR) = 0.93, 95% confidence interval (CI), 0.89-0.97] for men and 5% (RR = 0.95, 95% CI, 0.90-0.99) for women. All-cause mortality had a U-shaped association with adult height, the lowest risk occurring at 174 cm for men and 158 cm for women (both Pnonlinearity < 0.001). Relative to the shortest adult height (147 cm for men and 137 cm for women), men at 174 cm had a 47% lower likelihood of all-cause mortality and women at 158 cm a 33% lower risk of all-cause mortality.

CONCLUSIONS

Our study suggests that the relation between adult height and all-cause mortality is approximately U-shaped in both men and women.

Associations between genetic loci related to lean mass and body composition in type 2 diabetes

Aim

Several genetic loci related to lean mass have been identified in healthy individuals by genome‐wide association studies; however, the contribution of these loci to body composition in type 2 diabetes remains to be investigated. Here, we aimed to clarify the genetic determinants of body composition in individuals with type 2 diabetes.

Methods

A total of 176 Japanese outpatients (70 women and 106 men) with type 2 diabetes were studied using a cross‐sectional design. Body composition was measured using bioimpedance analysis with a commercially available device (InBody770). Single‐nucleotide polymorphisms in IRS1 (rs2943656), HSD17B11 (rs9991501), VCAN (rs2287926), ADAMTSL3 (rs4842924) and FTO (rs9936385) were evaluated by genotyping. The contributions of single‐nucleotide polymorphisms to body composition were examined, considering known clinical determinants.

Results

Sex, body composition and age were identified as clinical predictors. IRS1 rs2934656 was identified as an independent predictor of skeletal muscle mass (β = 0.11, P = 0.026), and ADAMTSL3 rs4842924 was an independent predictor of body fat mass (β = 0.15, P = 0.0095) and appendicular lean mass (β = −0.13, P = 0.017).

Conclusions

The findings clarified the contribution of genetic factors – IRS1 and ADAMTSL3 – to interindividual variation in body composition, independent of clinical factors, in type 2 diabetes patients. These data will contribute to the establishment of effective methods for the prediction, prevention, and intervention of sarcopenia and frailty in diabetes patients. Geriatr Gerontol Int 2021; 21: 932–938.

Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis

Coronary artery disease (CAD) genome-wide association studies typically focus on single nucleotide variants (SNVs), and many potentially associated SNVs fail to reach the GWAS significance threshold. We performed gene and pathway-based association (GBA) tests on publicly available Coronary ARtery DIsease Genome wide Replication and Meta-analysis consortium Exome (n = 120,575) and multi ancestry pan UK Biobank study (n = 442,574) summary data using versatile gene-based association study (VEGAS2) and Multi-marker analysis of genomic annotation (MAGMA) to identify novel genes and pathways associated with CAD. We included only exonic SNVs and excluded regulatory regions. VEGAS2 and MAGMA ranked genes and pathways based on aggregated SNV test statistics. We used Bonferroni corrected gene and pathway significance threshold at 3.0 × 10^-6 and 1.0 × 10^-5, respectively. We also report the top one percent of ranked genes and pathways. We identified 17 top enriched genes with four genes (PCSK9, FAM177, LPL, ARGEF26), reaching statistical significance (p ≤ 3.0 × 10^-6) using both GBA tests in two GWAS studies. In addition, our analyses identified ten genes (DUSP13, KCNJ11, CD300LF/RAB37, SLCO1B1, LRRFIP1, QSER1, UBR2, MOB3C, MST1R, and ABCC8) with previously unreported associations with CAD, although none of the single SNV associations within the genes were genome-wide significant. Among the top 1% non-lipid pathways, we detected pathways regulating coagulation, inflammation, neuronal aging, and wound healing.

Altered Ocular Fibrillin Microfibril Composition in Mice With a Glaucoma-Causing Mutation of Adamts10

Purpose

Previously, we identified a G661R mutation of ADAMTS10 (a disintegrin-like and metalloprotease with thrombospondin type 1 motif 10) as being disease causative in a colony of Beagles with inherited primary open-angle glaucoma (POAG). Mutations in ADAMTS10 are known to cause Weill-Marchesani syndrome (WMS), which is also caused by mutations in the fibrillin-1 gene (FBN1), suggesting functional linkage between ADAMTS10 and fibrillin-1, the principal component of microfibrils. Here, we established a mouse line with the G661R mutation of Adamts10 (Adamts10G661R/G661R) to determine if they develop features of WMS and alterations of ocular fibrillin microfibrils.

Methods

Intraocular pressure (IOP) was measured using a TonoLab rebound tonometer. Central cornea thickness (CCT), anterior chamber depth (ACD) and axial length (AL) of the eye were examined by spectral-domain optical coherence tomography. Sagittal eye sections from mice at postnatal day 10 (P10) and at 3 and 24 months of age were stained with antibodies against fibrillin-1, fibrillin-2, and ADAMTS10.

Results

IOP was not elevated in Adamts10G661R/G661R mice. Adamts10G661R/G661R mice had smaller bodies, thicker CCT, and shallower ACD compared to wild-type mice but normal AL. Adamts10G661R/G661R mice displayed persistent fibrillin-2 and enhanced fibrillin-1 immunofluorescence in the lens zonules and in the hyaloid vasculature and its remnants in the vitreous.

Conclusions

Adamts10G661R/G661R mice recapitulate the short stature and ocular phenotypes of WMS. The altered fibrillin-1 and fibrillin-2 immunoactivity in Adamts10G661R/G661R mice suggests that the G661R mutation of Adamts10 perturbs regulation of the fibrillin isotype composition of microfibrils in the mouse eye.

Determination of shared genetic etiology and possible causal relations between tobacco smoking and depression

BACKGROUNDS

Cigarette smoking is strongly associated with major depressive disorder (MDD). However, any genetic etiology of such comorbidity and causal relations is poorly understood, especially at the genome-wide level.

METHODS

In the present in silico research, we analyzed summary data from the genome-wide association study of the Psychiatric Genetic Consortium for MDD (n = 191 005) and UK Biobank for smoking (n = 337 030) by using various biostatistical methods including Bayesian colocalization analysis, LD score regression, variant effect size correlation analysis, and Mendelian randomization (MR).

RESULTS

By adopting a gene prioritization approach, we identified 43 genes shared by MDD and smoking, which were significantly enriched in membrane potential, gamma-aminobutyric acid receptor activity, and retrograde endocannabinoid signaling pathways, indicating that the comorbid mechanisms are involved in the neurotransmitter system. According to linkage disequilibrium score regression, we found a strong positive correlation between MDD and current smoking (rg = 0.365; p = 7.23 × 10-25) and a negative correlation between MDD and former smoking (rg = -0.298; p = 1.59 × 10-24). MR analysis suggested that genetic liability for depression increased smoking.

CONCLUSIONS

These findings inform the concomitant conditions of MDD and smoking and support the use of self-medication with smoking to counteract depression.