Specific Genetic Variants Research Articles

Molecular identification of Eurycoma longifolia Jack from Sumatra, Indonesia using trnL-F region

Abstract. Yulita KS, Susilowati A, Rachmat HH, Susila, Hidayat A, Dwiyanti FG. 2022. Molecular identification of Eurycoma longifolia Jack from Sumatra, Indonesia using trnL-F region. Biodiversitas 23: 1374-1382. Eurycoma longifolia Jack (Simaroubaceae) or pasak bumi is a popular medicinal plant from Southeast Asia’s rainforests that is used as an aphrodisiac, antimicrobial, anti-malaria antidiabetic, antiulcer, and anticancer agent. However, the increasing demand for this species for medicinal industries has led to illegal export in Indonesia. This study aimed to determine the specific genetic variation and develop DNA barcode using trnL-Fregion for E. longifolia originating from Sumatra, Indonesia. Twenty-two samples of the species were collected from four locations in Sumatra. An aligned sequence of the trnL-Fwas 960 bp with an A/T rich region (A: 30.2%, T: 34.5%, C: 16.7%, and G: 18.7%). The homology search using BLASTn of the GenBank NCBI showed that the nucleotide composition of the species was similar (99.9%) to the partial trnL-Fregion of E. longifolia MH751519 and E. apiculata GU593014. Close examination of the gene structure and composition showed that the DNA sequences have five nucleotides variations that were not possessed by the reference E. longifolia, and other taxa used. The obtained variations occurred mostly in the trnL intron region, and the phylogenetic analysis showed that the correct identity of the species of the samples by their position was at a similar clade as the other accessions of E. longifolia.

Boosting Schizophrenia Genetics by Utilizing Genetic Overlap With Brain Morphology

BackgroundSchizophrenia is a complex polygenic disorder with subtle, distributed abnormalities in brain morphology. There are indications of shared genetic architecture between schizophrenia and brain measures despite low genetic correlations. Through the use of analytical methods that allow for mixed directions of effects, this overlap may be leveraged to improve our understanding of underlying mechanisms of schizophrenia and enrich polygenic risk prediction outcome. MethodsWe ran a multivariate genome-wide analysis of 175 brain morphology measures using data from 33,735 participants of the UK Biobank and analyzed the results in a conditional false discovery rate together with schizophrenia genome-wide association study summary statistics of the Psychiatric Genomics Consortium (PGC) Wave 3. We subsequently created a pleiotropy-enriched polygenic score based on the loci identified through the conditional false discovery rate approach and used this to predict schizophrenia in a nonoverlapping sample of 743 individuals with schizophrenia and 1074 healthy controls. ResultsWe found that 20% of the loci and 50% of the genes significantly associated with schizophrenia were also associated with brain morphology. The conditional false discovery rate analysis identified 428 loci, including 267 novel loci, significantly associated with brain-linked schizophrenia risk, with functional annotation indicating high relevance for brain tissue. The pleiotropy-enriched polygenic score explained more variance in liability than conventional polygenic scores across several scenarios. ConclusionsOur results indicate strong genetic overlap between schizophrenia and brain morphology with mixed directions of effect. The results also illustrate the potential of exploiting polygenetic overlap between brain morphology and mental disorders to boost discovery of brain tissue–specific genetic variants and its use in polygenic risk frameworks.

Clinical Characterization of Copy Number Variants Associated With Neurodevelopmental Disorders in a Large-scale Multiancestry Biobank

Past studies identified rare copy number variants (CNVs) as risk factors for neurodevelopmental disorders (NDDs), including autism spectrum disorder and schizophrenia. However, the clinical characterization of NDD CNVs is understudied in population cohorts unselected for neuropsychiatric disorders and in cohorts of diverse ancestry. To identify individuals harboring NDD CNVs in a multiancestry biobank and to query their enrichment for select neuropsychiatric disorders as well as association with multiple medical disorders. In a series of phenotypic enrichment and association analyses, NDD CNVs were clinically characterized among 24 877 participants in the BioMe biobank, an electronic health record-linked biobank derived from the Mount Sinai Health System, New York, New York. Participants were recruited into the biobank since September 2007 across diverse ancestry and medical and neuropsychiatric specialties. For the current analyses, electronic health record data were analyzed from May 2004 through May 2019. NDD CNVs were identified using a consensus of 2 CNV calling algorithms, based on whole-exome sequencing and genotype array data, followed by novel in-silico clinical assessments. Of 24 877 participants, 14 586 (58.7%) were female; self-reported ancestry categories included 5965 (24.0%) who were of African ancestry, 7892 (31.7%) who were of European ancestry, and 8536 (34.3%) who were of Hispanic ancestry; and the mean (SD) age was 50.5 (17.3) years. Among 24 877 individuals, the prevalence of 64 NDD CNVs was 2.5% (n = 627), with prevalence varying by locus, corroborating the presence of some relatively highly prevalent NDD CNVs (eg, 15q11.2 deletion/duplication). An aggregate set of NDD CNVs were enriched for congenital disorders (odds ratio, 2.0; 95% CI, 1.1-3.5; P = .01) and major depressive disorder (odds ratio, 1.5; 95% CI, 1.1-2.0; P = .01). In a meta-analysis of medical diagnoses (n = 195 hierarchically clustered diagnostic codes), NDD CNVs were significantly associated with several medical outcomes, including essential hypertension (z score = 3.6; P = 2.8 × 10-4), kidney failure (z score = 3.3; P = 1.1 × 10-3), and obstructive sleep apnea (z score = 3.4; P = 8.1 × 10-4) and, in another analysis, morbid obesity (z score = 3.8; P = 1.3 × 10-4). Further, NDD CNVs were associated with increased body mass index in a multiancestry analysis (β = 0.19; 95% CI, 0.10-0.31; P = .003). For 36 common serum tests, there was no association with NDD CNVs. Clinical features of individuals harboring NDD CNVs were elucidated in a large-scale, multiancestry biobank, identifying enrichments for congenital disorders and major depressive disorder as well as associations with several medical outcomes, including hypertension, kidney failure, and obesity and obesity-related phenotypes, specifically obstructive sleep apnea and increased body mass index. The association between NDD CNVs and obesity outcomes indicate further potential pleiotropy of NDD CNVs beyond neurodevelopmental outcomes previously reported. Future clinical genetic investigations may lead to insights of at-risk individuals and therapeutic strategies targeting specific genetic variants. The importance of diverse inclusion within biobanks and considering the effect of rare genetic variants in a multiancestry context is evident.

Disease consequences of higher adiposity uncoupled from its adverse metabolic effects using Mendelian randomisation.

Some individuals living with obesity may be relatively metabolically healthy, whilst others suffer from multiple conditions that may be linked to adverse metabolic effects or other factors. The extent to which the adverse metabolic component of obesity contributes to disease compared to the non-metabolic components is often uncertain. We aimed to use Mendelian randomisation (MR) and specific genetic variants to separately test the causal roles of higher adiposity with and without its adverse metabolic effects on diseases. We selected 37 chronic diseases associated with obesity and genetic variants associated with different aspects of excess weight. These genetic variants included those associated with metabolically 'favourable adiposity' (FA) and 'unfavourable adiposity' (UFA) that are both associated with higher adiposity but with opposite effects on metabolic risk. We used these variants and two sample MR to test the effects on the chronic diseases. MR identified two sets of diseases. First, 11 conditions where the metabolic effect of higher adiposity is the likely primary cause of the disease. Here, MR with the FA and UFA genetics showed opposing effects on risk of disease: coronary artery disease, peripheral artery disease, hypertension, stroke, type 2 diabetes, polycystic ovary syndrome, heart failure, atrial fibrillation, chronic kidney disease, renal cancer, and gout. Second, 9 conditions where the non-metabolic effects of excess weight (e.g. mechanical effect) are likely a cause. Here, MR with the FA genetics, despite leading to lower metabolic risk, and MR with the UFA genetics, both indicated higher disease risk: osteoarthritis, rheumatoid arthritis, osteoporosis, gastro-oesophageal reflux disease, gallstones, adult-onset asthma, psoriasis, deep vein thrombosis, and venous thromboembolism. Our results assist in understanding the consequences of higher adiposity uncoupled from its adverse metabolic effects, including the risks to individuals with high body mass index who may be relatively metabolically healthy. Diabetes UK, UK Medical Research Council, World Cancer Research Fund, National Cancer Institute.

Prevalence of targeted therapy-related genetic variations in NSCLC and their relationship with clinicopathological characteristics.

Non-small cell lung cancer (NSCLC) is the most common cancer type in China. Targeted therapies have been used to treat NSCLC for two decades, which is only suitable for a subgroup of patients with specific genetic variations. The aim of this study was to investigate the prevalence of genetic variations leading to sensitivity or resistance to targeted therapies in NSCLC, and their relationship with clinicopathological characteristics of the patients. Tumor samples were collected from 404 patients who were diagnosed to have NSCLC and underwent surgery, transthoracic biopsy, bronchoscopy biopsy, or pleural aspiration in Sichuan Provincial People's Hospital from January 2019 to March 2020. Commercial amplification-refractory mutation system kits were used to detect targeted therapy-related genetic variations in those tumor samples. The prevalence of genetic variations and their relationship with patient clinicopathological characteristics were analyzed using statistical software, followed by subgroup analysis. In all, 50.7% of the NSCLC patients had sensitive genetic variations to anti-EGFR therapies, and 4.9% of those patients had co-existing resistant genetic variations. Fusions in ALK, ROS1, or RET were found in 7.7% of the patients, including 2 patients with co-existing EGFR exon 19 deletion or L858R. EGFR exon 19 deletion and L858R were more common in female patients and adenocarcinoma. Further subgroup analysis confirmed the observation in female patients in adenocarcinoma subgroup, and in adenocarcinoma in male patients. In addition, smokers were more likely to have squamous cell carcinoma and KRAS mutation and less likely to have EGFR L858R, which were also confirmed after standardization of gender except KRAS mutations. Nearly half of the NSCLC patients were eligible for anti-EGFR treatments. In NSCLC, female gender and adenocarcinoma may indicate higher chance of EGFR exon 19 deletion or L858R, and smoking history may indicate squamous cell carcinoma and EGFR L858R.

A single nonsynonymous mutation on ZIKV E protein-coding sequences leads to markedly increased neurovirulence in vivo.

Zika virus (ZIKV) can infect a wide range of tissues including the developmental brain of human fetus. Whether specific viral genetic variants are linked to neuropathology is incompletely understood. To address this, we have intracranially serially passaged a clinical ZIKV isolate (SW01) in neonatal mice and discovered variants that exhibit markedly increased virulence and neurotropism. Deep sequencing analysis combining with molecular virology studies revealed that a single 67D (Aspartic acid) to N (Asparagine) substitution on E protein is sufficient to confer the increased virulence and neurotropism in vivo. Notably, virus clones with D67N mutation had higher viral production and caused more severe cytopathic effect (CPE) in human neural astrocytes U251 ​cells in vitro, indicating its potential neurological toxicity to human brain. These findings revealed that a single mutation D67N on ZIKV envelope may lead to severe neuro lesion that may help to explain the neurovirulence of ZIKV and suggest monitoring the occurrence of this mutation during nature infection may be important.

Giardia duodenalis in Wildlife: Exploring Genotype Diversity in Italy and across Europe.

Fragmented data are so far available on genotype diversity of G. duodenalis in wildlife in different countries in Europe, in particular, in Italy. In the present study, G. duodenalis sequences obtained from different Italian wild animals [12 porcupines (Hystrix cristata), 4 wild boars (Sus scrofa), 1 wolf (Canis lupus italicus), 6 Alpine chamois (Rupicapra rupicapra rupicapra)] were compared with those available from wild host species in Europe to add new data on the geographic distribution of Giardia assemblages/sub-assemblages and their transmission patterns among natural hosts. Thirty-eight sequences were obtained by MLG analysis (SSU-rRNA, bg, gdh, and tpi genes) and subsequently compared by phylogenetic and network analyses with those from wild species monitored in the last decades in Europe. The results revealed the presence of potentially zoonotic (A-AI, A-AII from wild boar; B from porcupine) and host-adapted (D from wolf; E, A-AIII from chamois) assemblages and sub-assemblages and represent the first report for Italian wild boar. The analysis did not find any evidence of spatial or host segregation for specific genetic variants, mostly shared between different hosts from different European countries. However, conflicting evidence was found in genotypic assignment, advocating for data improvement and new genomic approaches.

Gene-Environment Interaction Analysis Incorporating Sex, Cardiometabolic Diseases, and Multiple Deprivation Index Reveals Novel Genetic Associations With COVID-19 Severity.

Increasing evidence indicates that specific genetic variants influence the severity of outcomes after infection with COVID-19. However, it is not clear whether the effect of these genetic factors is independent of the risk due to more established non-genetic demographic and metabolic risk factors such as male sex, poor cardiometabolic health, and low socioeconomic status. We sought to identify interactions between genetic variants and non-genetic risk factors influencing COVID-19 severity via a genome-wide interaction study in the UK Biobank. Of 378,051 unrelated individuals of European ancestry, 2,402 were classified as having experienced severe COVID-19, defined as hospitalization or death due to COVID-19. Exposures included sex, cardiometabolic risk factors [obesity and type 2 diabetes (T2D), tested jointly], and multiple deprivation index. Multiplicative interaction was tested using a logistic regression model, conducting both an interaction test and a joint test of genetic main and interaction effects. Five independent variants reached genome-wide significance in the joint test, one of which also reached significance in the interaction test. One of these, rs2268616 in the placental growth factor (PGF) gene, showed stronger effects in males and in individuals with T2D. None of the five variants showed effects on a similarly-defined phenotype in a lookup in the COVID-19 Host Genetics Initiative. These results reveal potential additional genetic loci contributing to COVID-19 severity and demonstrate the value of including non-genetic risk factors in an interaction testing approach for genetic discovery.

Whole-Genome Genotyping Using DNA Microarrays for Population Genetics.

The field of population genetics has exploded in the last two decades following the sequencing of the human genome in 2001 (Green et al. Nature 526:29-31, 2015). Tools to measure genetic variation have matured significantly throughout this advancement in knowledge (Lenoir and Giannella. J Biomed Discov Collab 1:11, 2006; Marzancola et al. Methods Mol Biol 1368:161-178, 2016). In this chapter, the focus is on the laboratory methods developed to perform genome-wide genotyping utilizing DNA microarrays, which is one of the most commonly used molecular techniques to assess global genetic variation (Heller MJ, Annu Rev Biomed Eng 4:129-153, 2002). DNA microarrays allow for the interrogation of hundreds of thousands of SNPs (single nucleotide polymorphisms) at once utilizing array-based technology in conjunction with fluorescent molecular labels in a process referred to as genotyping (Marzancola et al. Methods Mol Biol 1368:161-178, 2016). Genotype data can be utilized to associate certain phenotypes in relation with specific genetic variants within a population in a process known as genome-wide association studies or GWAS (Charlesworth and Charlesworth. Heredity (Edinb) 118(1):2-9, 2017; Casillas and Barbadilla. Genetics 205(3):1003-1035, 2017). This experimental technique is a multiple-day process involving the combination of DNA extraction, amplification, fragmentation, binding, and staining (Illumina Infinium HTS Assay Protocol Guide, 2013). Many vendors supply platforms and products to assess global genetic variation using DNA microarrays (Illumina Infinium HTS Assay Protocol Guide, 2013). In this chapter, the focus is on the methods utilized to generate high-quality genotype data with the Illumina® Infinium Global Screening Array. Although data analysis and quality control are not the focus for this chapter, they are also briefly addressed.

Analysis of EZH2 Genetic Variants on Triple-Negative Breast Cancer Susceptibility and Pathology.

Triple-negative breast cancer (TNBC) is the third most common female cancer in Taiwan. EZH2 plays an important role in cancer development through transcriptional repression by chromatin remodeling. However, the expression of EZH2 in breast cancer is highly correlated with tumorigenesis, and patient survival is not matched to TNBC. Furthermore, it has not been determined if specific EZH2 genetic variants are associated with breast cancer risk. In this paper, we evaluated the survival of different types of breast cancer. The results indicated that a lower expression of EZH2 led to poor survival of TNBC patients. Therefore, we aimed at studying the relationship between genetic polymorphisms of EZH2 and susceptibility to TNBC in Taiwan. Four single-nucleotide polymorphisms (SNPs) of EZH2 (rs6950683, rs2302427, rs3757441, and rs41277434) were analyzed by real-time PCR genotyping in 176 patients with TNBC and 1000 cancer-free controls. The results showed that TNBC patients under 60 years old who carried a TC or CC genotype at EZH2 rs6950683 and re3757441 had a tumor size of 20 mm or smaller (T1). Thus, this study is the first to examine the age and mutant genes associated with EZH2 SNPs in TNBC progression and development in Taiwan.

The role of nutrigenetics and nutrigenomics in the prophylaxis of chronic non-communicable diseases

Over the past several decades there has been an increase in the number of chronic noncommunicable diseases worldwide largely due to changes in diet and lifestyle, as well as exposure to adverse environmental factors. The so-called omics technologies (genomic, proteomic, metabolomic and transcriptomic) are used as tools for comprehensive analysis and monitoring of human health. Currently, genomic and post-genomic technologies are used to study the effects of various nutrients on human health. The purpose of the review was to summarize and analyze modern omics technologies used in the prevention of non-communicable diseases associated with human dietary habits. Material and methods. The literature search was carried out using PubMed, eLibrary, ResearchGate and ScienceDaily databases using the keywords "nutrigenetics", "nutrigenomics", "SNP", as well as the names of specific factors, genes and diseases. Results. The review provides up-to-date information on the role of knowledge of nutrigenetics and nutrigenomics in the prevention of chronic non-communicable diseases. Examples of the influence of specific single-nucleotide polymorphisms and genetic variations on various aspects of nutrition are given, from which recommendations for correcting the diet of carriers of these alleles to reduce the risk of cardiovascular diseases, type 2 diabetes mellitus, and obesity follow. Examples of nutrient influence on gene expression are also given and some genetic markers of metabolic disorders which can lead to diseases such as type 2 diabetes mellitus, obesity, inflammatory diseases of the colon, cardiovascular and neurodegenerative diseases, cancer are listed. Recommendations are given on the practical use of the knowledge gained during nutrigenomic studies on the effect of nutrient intake on the risk of non-communicable diseases for their prevention. Conclusion. The practical use of omics technologies can provide a more effective prevention of non-communicable diseases, contributing to an increase in the quality of life and the preservation of labor longevity of the population.

Precision Medicine Shows Promise to Advance the Care of Individuals with Hearing Loss

Hearing loss (HL) is the most common sensory disorder worldwide and arises from a heterogeneous set of genetic and environmental etiologies. Currently, therapy for sensorineural HL is non-specific and limited to amplification devices and implanted neuroprosthetics. Recent advances in the burgeoning field of precision medicine focused on individualizing disease diagnosis and tailoring treatment to each patient’s own biology hold great promise to provide tailored care for hearing loss patients. In this review, we discuss the current diagnostic algorithm and treatment options for hearing loss, the advances in using precision medicine tools to identify specific genetic variants that predispose to or result in hearing loss, the role of genetics in determining surgical outcomes following cochlear implantation, recent advances in gene and stem cell therapies for treating hearing loss, and patient-specific disease modeling using induced pluripotent stem cells. All of these precision medicine techniques will result in improved care for patients based on the precise etiology of their hearing loss.

Childhood traumatic events and the dopaminergic theory of psychosis: A mini-review of studies investigating gene – environment interactions

There is great body of evidence showing a relationship between childhood adversity and psychosis onset. Genetic factors moderate the association between childhood adversity and psychosis risk potentially by influencing biological and/or psychological reaction following exposure to adversity. In this review, we discuss studies identifying the specific genetic variants known to affect dopamine levels involved in this interaction. Our review shows that the catechol-O-methyltransferase (COMT), dopamine D2 receptor (DRD2), AKT1 gene play a key role in mediating the relationship between childhood adversity and development of psychosis. We have also found conflicting findings on the impact of dopamine genes on the relationship between childhood adversity and development of psychosis, suggesting that other genetic and environmental factors should be taken into account. We here discuss the implications of our findings and future directions.

Pharmacogenetics-based personalized treatment in patients with inflammatory bowel disease: A review

The development of treatment options has revolutionized the prognosis of inflammatory bowel disease (IBD). However, a particular group of patients still experience therapeutic failure or drug side effects. Although the high inter-patient variability in therapy is associated with clinical factors, including age, disease behavior, and disease duration, they attribute only a small proportion of inter-individual variability. Thus, pharmacogenetics evaluating associations between specific genetic variations and drug responses or side effects have focused on optimizing therapeutic efficacy and minimizing toxicity in IBD treatment. Thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) are well-established predictive markers of thiopurine-induced myelosuppression. Low TPMT activity is related to increased 6-thioguanine nucleotide levels, subsequently leading to myelotoxicity. NUDT15 variants are strongly associated with thiopurine-induced early leukopenia in Asians, with a lower incidence of TPMT-deficient allele. The Korean Association for the Study of Intestinal Diseases guidelines recommend pretreatment determination of NUDT15 genotypes, especially in East Asians, and NUDT15 R139C measurement has been approved for clinical use since 2019. Several studies have attempted to identify powerful genetic markers for personalized medicine. In this article, we review the identified pharmacogenetics of currently available drugs, focusing on 5-aminosalicylic acid, glucocorticosteroids, thiopurines, and anti-tumor necrosis factor-alpha agents.

Genetic effects on educational attainment in Hungary.

IntroductionEducational attainment is a substantially heritable trait, and it has recently been linked to specific genetic variants by genome‐wide association studies (GWASs). However, the effects of such genetic variants are expected to vary across environments, including countries and historical eras.MethodsWe used polygenic scores (PGSs) to assess molecular genetic effects on educational attainment in Hungary, a country in the Central Eastern European region where behavioral genetic studies are in general scarce and molecular genetic studies of educational attainment have not been previously published.ResultsWe found that the PGS is significantly associated with the attainment of a college degree as well as the number of years in education in a sample of Hungarian study participants (N = 829). PGS effect sizes were not significantly different when compared to an English (N = 976) comparison sample with identical measurement protocols. In line with previous Estonian findings, we found higher PGS effect sizes in Hungarian, but not in English participants who attended higher education after the fall of Communism, although we lacked statistical power for this effect to reach significance.DiscussionOur results provide evidence that polygenic scores for educational attainment have predictive value in culturally diverse European populations.

Long-read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds.

Advances in long-read sequencing technology and genome assembly provide an opportunity to improve the pig genome and reveal the full range of structural variations (SVs) between local Chinese and European pigs. To date, little is known about the genomes of some unique Chinese indigenous breeds, such as the Ningxiang pig. Here, we report the sequencing and assembly of a highly contiguous Ningxiang pig genome (NX) via an integration of PacBio single-molecule real-time sequencing, Illumina next-generation sequencing, BioNano optical mapping and Hi-C (chromosome conformation capture) approaches. The assembled genome comprises 2.44Gb with a contig N50 of 26.1Mb and 418 contigs in total. These contigs are organized into 121 scaffolds with a scaffold N50 of 139.0Mb. More than 99.1% of the assembled sequence could be localized to 19 pseudochromosomes and is annotated with 20,914 protein-coding genes and 34.04% repetitive sequences. Comparisons between the NX and European Duroc assemblies revealed many SVs in genes involved in the immune system, nervous system, lipid metabolism and environmental adaptation. The genetic variants include 47 Chinese domestic pig-specific SVs and the associated 74 genes may contribute to the differences in domestic traits compared to European pigs. Moreover, single nucleotide polymorphisms (SNPs) identified from whole genome resequencing data of 73 Chinese pigs, representing 17 geographically isolated breeds, showed their specific genetic variations, population structure and evolutionary patterns. Finally, we explore transcriptional regulation in the first intron of the MYL4 gene, as the genomic SV (281-bp deletion) in Ningxiang pig promotes its subcutaneous fat compared to European pig breeds. This work identifies a set of Asian-specific SVs and SNPs, which will be important resources for modern pig breeding and genetic conservation.

Identification of rare genetic variants of the αS-caseins in milk from native Norwegian dairy breeds and comparison of protein composition with milk from high-yielding Norwegian Red cows

Several factors influence the composition of milk. Among these, genetic variation within and between cattle breeds influences milk protein composition, protein heterogeneity, and their posttranslational modifications. Such variations may further influence technological properties, which are of importance for the utilization of milk into dairy products. Furthermore, these potential variations may also facilitate the production of differentiated products (e.g., related to specific breeds or specific genetic variants). The objective of this study was to investigate the genetic variation and relative protein composition of the major proteins in milk from 6 native Norwegian dairy breeds representing heterogeneity in geographical origin, using the modern Norwegian breed, Norwegian Red, as reference. In total, milk samples from 144 individual cows were collected and subjected to liquid chromatography-electrospray ionization/mass spectrometry-based proteomics for identification of genetic and posttranslational modification isoforms of the 4 caseins (αS1-CN, αS2-CN, β-CN, κ-CN) and the 2 most abundant whey proteins (α-lactalbumin and β-lactoglobulin). Relative quantification of these proteins and their major isoforms, including phosphorylations of αS1-CN and glycosylation of κ-CN, were determined based on UV absorbance. The presence and frequency of genetic variants of the breeds were found to be very diverse and it was possible to identify rare variants of the CN, which, to our knowledge, have not been identified in these breeds before. Thus, αS1-CN variant D was identified in low frequency in 3 of the 6 native Norwegian breeds. In general, αS1-CN was found to be quite diverse between the native breeds, and the even less frequent A and C variants were furthermore detected in 1 and 5 of the native breeds, respectively. The αS1-CN variant C was also identified in samples from the Norwegian Red cattle. The variant E of κ-CN was identified in 2 of the native Norwegian breeds. Another interesting finding was the identification of αS2-CN variant D, which was found in relatively high frequencies in the native breeds. Diversity in more common protein genetic variants were furthermore observed in the protein profiles of the native breeds compared with milk from the high-yielding Norwegian Reds, probably reflecting the more diverse genetic background between the native breeds.

Constructing a polygenic risk score for childhood obesity using functional data analysis

Obesity is a highly heritable condition that affects increasing numbers of adults and, concerningly, of children. However, only a small fraction of its heritability has been attributed to specific genetic variants. These variants are traditionally ascertained from genome-wide association studies (GWAS), which utilize samples with tens or hundreds of thousands of individuals for whom a single summary measurement (e.g., BMI) is collected. An alternative approach is to focus on a smaller, more deeply characterized sample in conjunction with advanced statistical models that leverage longitudinal phenotypes. Novel functional data analysis (FDA) techniques are used to capitalize on longitudinal growth information from a cohort of children between birth and three years of age. In an ultra-high dimensional setting, hundreds of thousands of single nucleotide polymorphisms (SNPs) are screened, and selected SNPs are used to construct two polygenic risk scores (PRS) for childhood obesity using a weighting approach that incorporates the dynamic and joint nature of SNP effects. These scores are significantly higher in children with (vs. without) rapid infant weight gain—a predictor of obesity later in life. Using two independent cohorts, it is shown that the genetic variants identified in very young children are also informative in older children and in adults, consistent with early childhood obesity being predictive of obesity later in life. In contrast, PRSs based on SNPs identified by adult obesity GWAS are not predictive of weight gain in the cohort of young children. This provides an example of a successful application of FDA to GWAS. This application is complemented with simulations establishing that a deeply characterized sample can be just as, if not more, effective than a comparable study with a cross-sectional response. Overall, it is demonstrated that a deep, statistically sophisticated characterization of a longitudinal phenotype can provide increased statistical power to studies with relatively small sample sizes; and shows how FDA approaches can be used as an alternative to the traditional GWAS.

Extensive analysis of mitochondrial DNA quantity and sequence variation in human cumulus cells and assisted reproduction outcomes.

Are relative mitochondrial DNA (mtDNA) content and mitochondrial genome (mtGenome) variants in human cumulus cells (CCs) associated with oocyte reproductive potential and assisted reproductive technology (ART) outcomes? Neither the CC mtDNA quantity nor the presence of specific mtDNA genetic variants was associated with ART outcomes, although associations with patient body mass index (BMI) were detected, and the total number of oocytes retrieved differed between major mitochondrial haplogroups. CCs fulfil a vital role in the support of oocyte developmental competence. As with other cell types, appropriate cellular function is likely to rely upon adequate energy production, which in turn depends on the quantity and genetic competence of the mitochondria. mtDNA mutations can be inherited or they can accumulate in somatic cells over time, potentially contributing to aging. Such mutations may be homoplasmic (affecting all mtDNA in a cell) or they may display varying levels of heteroplasmy (affecting a proportion of the mtDNA). Currently, little is known concerning variation in CC mitochondrial genetics and how this might influence the reproductive potential of the associated oocyte. This was a prospective observational study involving human CCs collected with 541 oocytes from 177 IVF patients. mtDNA quantity was measured in all the samples with a validated quantitative PCR method and the entire mtGenome was sequenced in a subset of 138 samples using a high-depth massively parallel sequencing approach. Associations between relative mtDNA quantity and mtGenome variants in CCs and patient age, BMI (kg/m2), infertility diagnosis and ART outcomes were investigated. Massively parallel sequencing permitted not only the accurate detection of mutations but also the precise quantification of levels of mutations in cases of heteroplasmy. Sequence variants in the mtDNA were evaluated using Mitomaster and HmtVar to predict their potential impact. The relative mtDNA CC content was significantly associated with BMI. No significant associations were observed between CC mtDNA quantity and patient age, female infertility diagnosis or any ART outcome variable. mtGenome sequencing revealed 4181 genetic variants with respect to a reference genome. The COXI locus contained the least number of coding sequence variants, whereas ATPase8 had the most. The number of variants predicted to affect the ATP production differed significantly between mitochondrial macrohaplogroups. The total number of retrieved oocytes was different between the H-V and J-T as well as the U-K and J-T macrohaplogroups. There was a non-significant increase in mtDNA levels in CCs with heteroplasmic mitochondrial mutations. N/A. Although a large number of samples were analysed in this study, it was not possible to analyse all the CCs from every patient. Also, the results obtained with respect to specific clinical outcomes and macrohaplogroups should be interpreted with caution due to the smaller sample sizes when subdividing the dataset. These findings suggest that the analysis of mtDNA in CCs is unlikely to provide an advantage in terms of improved embryo selection during assisted reproduction cycles. Nonetheless, our data raise interesting biological questions, particularly regarding the interplay of metabolism and BMI and the association of mtDNA haplogroup with oocyte yield in ovarian stimulation cycles. This study was funded by National Institutes of Health grant 5R01HD092550-02. D.J.N. and C.R. co-hold patent US20150346100A1 and D.J.N. holds US20170039415A1, both for metabolic imaging methods. D.W. receives support from the NIHR Oxford Biomedical Research Centre. The remaining authors have no conflicts of interest to declare.

Brain Cancers in Genetic Syndromes.

Although genetic conditions that cause primary central nervous system tumors are rare, their pathophysiology influences both treatment and surveillance. This article reviews the most frequently occurring genetic conditions associated with brain cancers and highlights the most recent therapeutic approaches in the treatment of Lynch syndrome (and other disorders of the mismatch repair system), neurofibromatosis 1, and Li-Fraumeni syndrome. Recent advances in molecular diagnostics have considerably improved the ability to diagnose genetic conditions in people with primary brain tumors. The common application of next-generation sequencing analyses of tissue increases the frequency with which clinicians are forced to address the possibility of an underlying genetic condition based on tissue molecular findings. Clinicians must be aware of the clinical presentation of genetic conditions predisposing to brain tumors in order to discern which patients are appropriate for germline genetic testing. Advances in therapeutics for specific genetic variants are increasingly available, and accurately diagnosing an underlying genetic condition may directly impact patient outcomes.