Genome Project Research Articles

Association of Mitochondrial HVS-I Region Variants with Type 2 Diabetes in Pakistani Diabetic Subjects.

To analyse mitochondrial hypervariable segment I (HVS-I) variations in Pakistani type 2 diabetic subjects. Case-control study. Place and Duration of the Study: National Institute of Diabetes and Endocrinology, Dow University of Health Sciences, Karachi, Pakistan, between January 2019 to January 2021. DNA from whole blood was isolated, and mitochondrial HVS-I region (16024-16370) of 92 individuals, including 47 controls and 45 diabetics, was amplified, sequenced, and analysed. Ninety-two variable sites in the sequenced region were identified and individuals were classified into 56 different haplotypes according to phylotree 17.0 classifications, where major haplotype M5 was nearly 2-fold higher in diabetes. Fischer's exact test revealed variant 16189T>C significantly associated with diabetes (Odds ratio = 12.9, 95% CI = 0.6917 - 2400248) as compared to controls. The authors further analysed 1000 Genomes Project data of Pakistani Control subjects (i.e. PJL, n=96) and found that besides 16189T>C (Odds ratio = 5.875, 95% CI = 1.093 - 31.57, p<0.0339), 16264C>T (Odds ratio = 16, 95% CI = 0.8026 - 314.7, p<0.0310) also showed significant association with diabetic subjects. Comparing diabetic subject data with global control population data of the 1000 Genomes Project, significant associations of eight variants in the studied region were found. Based on the results of this case-control study, it can be concluded that specific variations in the mitochondrial hypervariable segment I (HVS-I) region are significantly associated with type 2 diabetes in the Pakistani population. The major haplotype M5 was found to be higher in diabetic subjects and variants 16189T>C and 16264C>T were significantly associated with diabetes. These findings suggest that mitochondrial DNA variations may play a role in the development of type 2 diabetes in the Pakistani population. Diabetes Mellitus, HVS-1 region, Diabetic subjects, Mitochondrial genomics, Pakistani population.

Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder

PurposeRPH3A encodes a protein involved in the stabilization of GluN2A subunit of N-methyl-D-aspartate (NMDA)-type glutamate receptors at the cell surface, forming a complex essential for synaptic plasticity and cognition. We investigated the effect of variants in RPH3A in patients with neurodevelopmental disorders. MethodsBy using trio-based exome sequencing, GeneMatcher, and screening of 100,000 Genomes Project data, we identified 6 heterozygous variants in RPH3A. In silico and in vitro models, including rat hippocampal neuronal cultures, have been used to characterize the effect of the variants. ResultsFour cases had a neurodevelopmental disorder with untreatable epileptic seizures [p.(Gln73His)dn; p.(Arg209Lys); p.(Thr450Ser)dn; p.(Gln508His)], and 2 cases [p.(Arg235Ser); p.(Asn618Ser)dn] showed high-functioning autism spectrum disorder. Using neuronal cultures, we demonstrated that p.(Thr450Ser) and p.(Asn618Ser) reduce the synaptic localization of GluN2A; p.(Thr450Ser) also increased the surface levels of GluN2A. Electrophysiological recordings showed increased GluN2A-dependent NMDA ionotropic glutamate receptor currents for both variants and alteration of postsynaptic calcium levels. Finally, expression of the Rph3AThr450Ser variant in neurons affected dendritic spine morphology. ConclusionOverall, we provide evidence that missense gain-of-function variants in RPH3A increase GluN2A-containing NMDA ionotropic glutamate receptors at extrasynaptic sites, altering synaptic function and leading to a clinically variable neurodevelopmental presentation ranging from untreatable epilepsy to autism spectrum disorder.

Genome-wide scans for selective sweeps using convolutional neural networks.

Recent methods for selective sweep detection cast the problem as a classification task and use summary statistics as features to capture region characteristics that are indicative of a selective sweep, thereby being sensitive to confounding factors. Furthermore, they are not designed to perform whole-genome scans or to estimate the extent of the genomic region that was affected by positive selection; both are required for identifying candidate genes and the time and strength of selection. We present ASDEC (https://github.com/pephco/ASDEC), a neural-network-based framework that can scan whole genomes for selective sweeps. ASDEC achieves similar classification performance to other convolutional neural network-based classifiers that rely on summary statistics, but it is trained 10× faster and classifies genomic regions 5× faster by inferring region characteristics from the raw sequence data directly. Deploying ASDEC for genomic scans achieved up to 15.2× higher sensitivity, 19.4× higher success rates, and 4× higher detection accuracy than state-of-the-art methods. We used ASDEC to scan human chromosome 1 of the Yoruba population (1000Genomes project), identifying nine known candidate genes.

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function.

Millions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently. We developed TransFun-a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating that the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy. The source code of TransFun is available at https://github.com/jianlin-cheng/TransFun.

Women's empowerment and child nutrition in a context of shifting livelihoods in Eastern Oromia, Ethiopia.

Agriculture, and particularly livestock and animal source foods, has been closely linked to improvements in human nutrition. Production, income, and women's empowerment improve household food security and child nutritional outcomes in interacting ways. Khat production in Eastern Ethiopia is changing the economic and livelihood landscape for communities that have traditionally relied upon small-scale mixed agriculture and livestock production. How this shifting livelihood landscape and the empowerment of women in these communities are affecting nutritional outcomes has not been investigated. Using cross-sectional data collected during formative research for the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) project, we developed models to examine the roles of livelihood activities, including livestock production, staple crop production, and khat production, and women's empowerment in child nutrition outcomes. Survey participants were randomly selected mothers of children aged 10-15 months from Haramaya district, Eastern Hararghe, Oromia, Ethiopia. Nested logistic regression models were performed for each nutrition outcome: children's animal source food consumption, children's dietary diversity, and child stunting, wasting, and underweight. Explanatory variables included those for livelihood (tropical livestock unit, crop production, and khat production ladder) and women's empowerment (as indicated by domains of the Women's Empowerment in Agriculture Index), and covariates including child sex, mother's age, mother's education, assets, income, and kebele. Results indicated that khat production and tropical livestock units were not significantly associated with any of the child nutrition outcomes. However, results did indicate that the odds of reporting child animal source food consumption in households where the mother was empowered in the leadership domain was 3.33 times that in households where the mother wasn't (p < 0.05). In addition, the odds of having a stunted child in households where the mother was empowered in the time domain was 2.68 times that in households where the mother wasn't (p < 0.05). The results from this study both support and complicate the existing literature on the associations between women's empowerment in agriculture and child nutrition outcomes, underscoring the important role that livelihood, contextual factors, and location may have on the complex relationship between empowerment domains and nutritional outcomes.

Genomic newborn screening for rare diseases.

Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.

CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data

Abstract Statistical tests for molecular evolution provide quantifiable insights into the selection pressures that govern a genome's evolution. Increasing sample sizes used for analysis leads to higher statistical power. However, this requires more computational nodes or longer computational time. CATE (CUDA Accelerated Testing of Evolution) is a computational solution to this problem comprised of two main innovations. The first is a file organization system coupled with a novel search algorithm and the second is a large‐scale parallelization of algorithms using both graphical processing unit (GPU) and central processing unit. CATE is capable of conducting evolutionary tests such as Tajima's D, Fu and Li's, and Fay and Wu's test statistics, McDonald–Kreitman Neutrality Index, Fixation Index and Extended Haplotype Homozygosity. CATE is magnitudes faster than standard tools with benchmarks estimating it being on average over 180 times faster. For instance, CATE processes all 54,849 human genes for all 22 autosomal chromosomes across the five super populations present in the 1000 Genomes Project in less than 30 min while counterpart software took 3.62 days. This proven framework has the potential to be adapted for GPU‐accelerated large‐scale parallel analyses of many evolutionary and genomic analyses.

Risk-conferring HLA variants in an epilepsy cohort: benefits of multifaceted use of whole genome sequencing in clinical practice

BackgroundWhole genome sequencing is increasingly used in healthcare, particularly for diagnostics. However, its clinically multifaceted potential for individually customised diagnostic and therapeutic care remains largely unexploited. We used existing whole...

BG01 Confirming small nuclear ribonucleoprotein polypeptide E as a cause of nonsyndromic hypotrichosis

Abstract Hereditary nonsyndromic hypotrichosis comprises at least 15 genetically distinct but phenotypically overlapping disorders. Affected individuals generally have hair at birth, which sheds during infancy or childhood. Severity ranges from partial alopecia to complete loss of scalp and body hair, with phenotypic variability between and within families. Genetic testing is essential for accurate diagnosis and counselling. We describe a case where several factors contributed to a delay in genetic diagnosis. A female child of nonconsanguineous White parents was born at term with normal hair that started to shed at 2 weeks of age. By 6 weeks of age, there was a complete absence of scalp, eyelash and eyebrow hair. There was no relevant family history apart from atopy. On examination at 3.3 years of age, she had total alopecia apart from some hairs in the external auditory canals. Nails, teeth and sweating were normal. She appeared developmentally normal and healthy apart from mild eczema with persistent erythema on both cheeks. The differential diagnosis included autoimmune alopecia and genetic nonsyndromic hypotrichosis. She was recruited to the 100 000 Genomes Project, but primary analysis did not identify any causative variants. Reanalysis using a limited gene-agnostic approach identified heterozygosity for the c.1A&amp;gt;G; p.(Met1?) variant in small nuclear ribonucleoprotein polypeptide E (SNRPE) that was not present in parents. This variant is not present in the gnomAD population database and is predicted to alter the initiation codon of SNRPE. It has been reported de novo in a British girl with sparse scalp hair and eyelashes and absent eyebrows, and in eight affected members of a Spanish family whose phenotypes ranged from sparse eyebrows and eyelashes to complete alopecia (Pasternack SM, Refke M, Paknia E et al. Mutations in SNRPE, which encodes a core protein of the spliceosome, cause autosomal dominant hypertrichosis simplex. Am J Hum Genet 2013; 92:81–7). This condition has been designated hypotrichosis type 11. SNRPE encodes a core protein of U small nuclear ribonucleoproteins, which are essential to the removal of introns from pre-mRNA and thus critical for the post-transcriptional modification of RNA. In our case, review of the primary analysis showed that the incorrect gene panel was applied (‘familial cicatricial alopecia’ instead of ‘nonsyndromic hypotrichosis’) and that SNRPE was listed as ‘amber’ for hypotrichosis, meaning ‘moderate evidence for this gene–disease association and should not yet be used for genome interpretation’. Genomics England has now incorporated nonsyndromic hypotrichosis into the ‘ectodermal dysplasia’ panel, with SNRPE now listed as ‘green’ for hypotrichosis 11, meaning a ‘high level of evidence for this gene–disease association’. This case emphasizes the importance of revisiting negative results as knowledge evolves.

An Updated Overview on Personalized Medicine: The Next-Gen Paradigm

Personalized medicine is a translational approach that utilizes an individual’s genetic profile to guide illness prevention, diagnosis, and treatment choices. The human genome project data is being used to enhance personalized treatment. “Personalised” medicine is beneficial over “individualized” medicine as it suggests that future hazards may be predicted based on the individual’s genes. The advancement of technology for personalized medicine depends heavily on standardization, integration, and harmonization. The scientific practices at various research sites, the connection between science and healthcare, and the relationship between science, healthcare, and broader society, including the legal and ethical paradigms, the dominant cultural and political ethos, and the expectations of patients and citizens - all need to be in harmony. There are several descriptions of the current existing legislation that regulates genetic screening and genomic medical services in various countries around the world, highlighting discrepancies and specifying areas of law where harmonization may be needed to enable the use of individually tailored medication globally. The promise of personalized medicine can only be fulfilled by placing the individual at the centre of personalized medicine and tailoring care to each patient’s unique psychological and social needs in addition to their biological profiles.

Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements.

Analyses of genetic variation in many taxa have established that neutral genetic diversity is shaped by natural selection at linked sites. Whether the mode of selection is primarily the fixation of strongly beneficial alleles (selective sweeps) or purifying selection on deleterious mutations (background selection) remains unknown, however. We address this question in humans by fitting a model of the joint effects of selective sweeps and background selection to autosomal polymorphism data from the 1000 Genomes Project. After controlling for variation in mutation rates along the genome, a model of background selection alone explains ~60% of the variance in diversity levels at the megabase scale. Adding the effects of selective sweeps driven by adaptive substitutions to the model does not improve the fit, and when both modes of selection are considered jointly, selective sweeps are estimated to have had little or no effect on linked neutral diversity. The regions under purifying selection are best predicted by phylogenetic conservation, with ~80% of the deleterious mutations affecting neutral diversity occurring in non-exonic regions. Thus, background selection is the dominant mode of linked selection in humans, with marked effects on diversity levels throughout autosomes.

Characterization of Reference Materials for CYP3A4 and CYP3A5: A (GeT-RM) Collaborative Project

Pharmacogenetic testing for CYP3A4 is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials are currently available for many of the CYP3A4 variants included in clinical tests. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program (GeT-RM), in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 30 DNA samples derived from Coriell cell lines for CYP3A4. Samples were distributed to five volunteer laboratories for genotyping using a variety of commercially available and laboratory-developed tests. Sanger and next-generation sequencing were also utilized by some of the laboratories. Whole-genome sequencing data from the 1000 Genomes Projects were utilized to inform genotype. Twenty CYP3A4 alleles were identified in the 30 samples characterized for CYP3A4: CYP3A4∗4, ∗5, ∗6, ∗7, ∗8, ∗9, ∗10, ∗11, ∗12, ∗15, ∗16, ∗18, ∗19, ∗20, ∗21, ∗22, ∗23, ∗24, ∗35, and a novel allele, CYP3A4∗38. Nineteen additional samples with preexisting data for CYP3A4 or CYP3A5 were re-analyzed to generate comprehensive reference material panels for these genes. These publicly available and well-characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing.

High throughput phenomics for diatoms: Challenges and solutions

Underpinning primary food chains, atmospheric carbon cycling, and vital ecosystem functions are diatoms, a class of microalgae found ubiquitously in aquatic environments around the globe (Armbrust, 2009; Nelson et al., 1995). As with most organisms on earth climate change threatens their survival and distribution, therefore their ability to adapt to environmental drivers through phenotypic plasticity has become a topic of investigation in recent years (Cox, 2014; Sackett et al., 2013; Vartanian et al., 2009). Furthermore, diatoms are being seen in a new light thanks to recent endeavours to unravel the genomes of a broad range of species across the phylogenetic tree, including the currently underway ‘100 Diatom Genome Project’ and the “Earth BioGenome Project” project which aims to sequence over 3000 protozoa (Bowler et al., 2008; Armbrust, 2009, Joint Genome Institute, 2021; Earth BioGenome Project, 2022; Mock et al., 2022). Knowing the genome is however insufficient in understanding the complex responsivity of an organism exposed to variable environmental conditions, and thus a large-scale diatom phenotyping project is needed. Embarking on such a project that involves a multitude of diverse and intricate organisms will undoubtedly pose challenges. These hurdles stem not only from their extensive genetic diversity, but also from the complex endeavour of consolidating their phenomes. In adapting modern phenomics methods to bridge the genome-phenome gap in diatoms, multi-driver and multi-trait relationships must be considered across a range of species, in which many phenotypes may be expressed under different conditions (Chitwood and Topp, 2015). Armed with comprehensive genomic and phenomic datasets for a range of diatoms, we may be able to predict with more precision the effects of climate change on ecological and biogeochemical processes that are driven by diatom primary productivity.

Reference genome of California walnut, Juglans californica, and resemblance with other genomes in the order Fagales.

Juglans californica, California walnut, is a vulnerable small tree that is locally abundant but restricted to woodland and chaparral habitats of Southern California threatened by urbanization and land use change. This species is the dominant species in a unique woodland ecosystem in California. It is one of two endemic California walnut species (family Juglandaceae). The other species, Northern California black walnut (J. hindsii), has been suggested controversially to be a variety of J. californica. Here, we report a new, chromosome-level assembly of J. californica as part of the California Conservation Genomics Project (CCGP). Consistent with the CCGP common methodology across ~150 genomes, we used Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 137 scaffolds spanning 551,065,703 base pairs, has a contig N50 of 30Mb, a scaffold N50 of 37Mb, and BUSCO complete score of 98.9%. Additionally, the mitochondrial genome has 701,569 base pairs. In addition, we compare this genome with other existing high quality Juglans and Quercus genomes, which are in the same order (Fagales) and show relatively high synteny within the Juglans genomes. Future work will utilize the J. californica genome to determine its relationship with the Northern California walnut and assess the extent to which these two endemic trees might be at risk from fragmentation and/or climate warming.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans.

Amyotrophic lateral sclerosis (ALS) is a degenerative condition of the brain and spinal cord in which protein-coding variants in known ALS disease genes explain a minority of sporadic cases. There is a growing interest in the role of noncoding structural variants (SVs) as ALS risk variants or genetic modifiers of ALS phenotype. In small European samples, specific short SV alleles in noncoding regulatory regions of SCAF4, SQSTM1, and STMN2 have been reported to be associated with ALS, and several groups have investigated the possible role of SMN1/SMN2 gene copy numbers in ALS susceptibility and clinical severity. Using short-read whole genome sequencing (WGS) data, we investigated putative ALS-susceptibility SCAF4 (3'UTR poly-T repeat), SQSTM1 (intron 5 AAAC insertion), and STMN2 (intron 3 CA repeat) alleles in African ancestry patients with ALS and described the architecture of the SMN1/SMN2 gene region. South African cases with ALS (n = 114) were compared with ancestry-matched controls (n = 150), 1000 Genomes Project samples (n = 2,336), and H3Africa Genotyping Chip Project samples (n = 347). There was no association with previously reported SCAF4 poly-T repeat, SQSTM1 AAAC insertion, and long STMN2 CA alleles with ALS risk in South Africans (p > 0.2). Similarly, SMN1 and SMN2 gene copy numbers did not differ between South Africans with ALS and matched population controls (p > 0.9). Notably, 20% of the African samples in this study had no SMN2 gene copies, which is a higher frequency than that reported in Europeans (approximately 7%). We did not replicate the reported association of SCAF4, SQSTM1, and STMN2 short SVs with ALS in a small South African sample. In addition, we found no link between SMN1 and SMN2 copy numbers and susceptibility to ALS in this South African sample, which is similar to the conclusion of a recent meta-analysis of European studies. However, the SMN gene region findings in Africans replicate previous results from East and West Africa and highlight the importance of including diverse population groups in disease gene discovery efforts. The clinically relevant differences in the SMN gene architecture between African and non-African populations may affect the effectiveness of targeted SMN2 gene therapy for related diseases such as spinal muscular atrophy.

#3166 RECOGNITION OF RENAL TUBULAR DYSGENESIS IN ADOLESCENT CKD BY BIALLELIC AGT VARIANTS REQUIRED BROAD GENETIC ANALYSIS

Abstract Background and Aims Autosomal recessive renal tubular dysgenesis (ARRTD) is a rare inherited disorder of renal (tubular) development, clinically characterized by fetal oligo-/anuria leading to oligohydramnion and Potter sequence, resulting in high mortality within the prenatal and neonatal period. Variants in genes encoding components of the renin-angiotensin system (RAS) are causative for this disorder. Herein, we report 2 European families with biallelic variants within AGT and aim to provide novel insides into disease understanding. Method The study was approved by our institutional ethics committee (approval number: 251_18 B). Clinical, histological and pedigree analysis were performed. Exome sequencing of a preselected gene panel (nephroma, 560 genes associated with renal disease) was analysed on the HiSeq System 2500 (Illumina) after enrichment by TWIST human core technology (TWIST Bioscience). Immunohistochemistry staining (IHC) and in-situ hybridization (ISH) for expression of renin were performed on kidney biopsy. In addition, renin expression was determined in primary tubular cells of the index patient by qPCR. Allele frequencies of heterozygous and biallelic predicted deleterious variants were determined by analysis of the Genomics England 100,000 Genomes Project. Results The first family was identified after transition from pediatric to adult nephrology at the University Hospital Erlangen. Initially, the male index patient of consanguineous Turkish descent presented with oligohydramnion in the prenatal period. Directly after birth (32nd gestational week) he suffered from profound hypotension, pulmonary hypoplasia and pulmonary stenosis, as well as third degree acute kidney injury leading to ICU treatment, but no need of hemodialysis. He survived the perinatal period while a decline in renal function was observed over time leading to CKD G3b at the age of 19 years. Exome sequencing revealed a previously reported pathogenic homozygous missense variant within AGT (c.1224G&amp;gt;A, p.Arg375Gln). Kidney biopsy at the age of 14 years revealed tubulointerstitial fibrosis, profound glomerulocystic changes with partly glomerulosclerosis and vasculopathic features. IHC and ISH showed recruitment and strong expression of renin in tubular cells and vessels, where cultured primary tubular cells also showed strong expression of renin. Circulating renin was profoundly elevated, with normal levels of aldosterone. The patient is not hypertensive and receives no antihypertensive medications. The family history revealed at least 2 miscarriages due to oligohydramnion. The second family was identified from the Genomics England 100,000 Genomes Project. The male index patient presented with prenatal bilateral hydronephrosis. He was delivered prematurely around the 35th gestational week. Both kidneys suffered from chronic bilateral urinary reflux leading to CKD G2 at the age of 8 years. Family history revealed one prior miscarriage. Genetic analysis revealed two compound heterozygous missense variants within AGT (c.842A&amp;gt;G, p.Tyr281Cys; c.151T&amp;gt;C, p.Cys51Arg). The heterozygous allele frequency in the Genomics England cohort for AGT predicted deleterious variants was very low. Therefore, we would predict a biallelic hit with the respective disease as an ultra-rare event. Reviewing the literature, to our knowledge 18 individuals are reported to date with different biallelic variants within AGT. From these cases only three survived the perinatal period. It is not reported if these individuals reached adulthood. Conclusion We hereby demonstrate two extremely rare cases, affected by biallelic variants within AGT, that survived the perinatal period and eventually led to chronic kidney disease. Since the phenotypes may be variable, a contemporary approach by broad genetic analysis is the only option to decode the genetic background in individuals with a suspected genetic disorder. Upregulation of renin in tubular cells by inactivation of AGT in the germline may drive tubulointerstitial fibrosis, which is a theoretical concern regarding ongoing targeted pharmacological approaches against AGT for arterial hypertension.

Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project.

In our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r2 = 0.18) and soil collected inside the house (r2 = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r2 < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.

OUTC-10. SELF-REPORTED RACE AND ETHNICITY AND GENETIC ANCESTRY GROUPS SHOW DISTINCT PREVALENCE AND OUTCOMES ACROSS PEDIATRIC CENTRAL NERVOUS SYSTEM TUMORS

Abstract BACKGROUND Race and ethnicity disparities have been identified in survival of pediatric central nervous system (CNS) tumors. No prior studies have investigated the comparative effects of self-identified race and ethnicity versus genetic ancestry on tumor prevalence and outcome. We examine these contributions in a retrospective analysis of pediatric patients with CNS tumors. METHODS Patients from Children’s Brain Tumor Network (CBTN; n=646) and Pacific Pediatric Neuro-Oncology Consortium (PNOC; n=35) with available clinical data and whole genome sequencing were included. Ancestry groups were predicted with somalier and genetic markers from reference individuals of known ancestry that participated in the 1000 Genomes Project: sub-Saharan African (AFR), admixed American (AMR), East Asian (EAS), European (EUR), and South Asian (SAS). Independence of predicted ancestry and self-reported race and ethnicity was assessed with chi-squared tests. Effects of predicted ancestry on survival were estimated using multivariate Cox models with molecular subtype and extent of tumor resection as covariates. RESULTS Predicted ancestry groups were highly concordant with self-reported race (χ2=897, p&amp;lt;0.001) and ethnicity (χ2=340, p&amp;lt;0.001). Patients from AFR ancestry were significantly enriched within ATRT (n=26; p=0.001) and neurofibroma plexiform (n=11; p=0.005) and patients with AMR ancestry were enriched within DMG (n=53; p&amp;lt;0.001). Patients diagnosed with H3 wildtype high-grade glioma (n=39) with non-EUR ancestry trended towards worse overall survival (OS; HR=2.0, p=0.07). Patients with ATRT (n=19) with AMR ancestry trended towards worse OS compared to AFRs (HR=4.1, p=0.09) and AFR patients with MB (n=78) trended toward worse OS compared to EUR patients (HR=3.7, p=0.07), including Group 4 MBs (n=39; HR=3.9, p=0.08). Patients with LGG (n=182) with non-EUR ancestry were more likely to have less than gross total/near total resection compared to patients with EUR ancestry (p=0.02). CONCLUSIONS Differences in ancestry are seen across pediatric CNS tumor entities and outcomes. Analyses are underway in an additional ~800 patients.

A genotype-to-phenotype approach suggests under-reporting of single nucleotide variants in nephrocystin-1 (NPHP1) related disease (UK 100,000 Genomes Project)

Autosomal recessive whole gene deletions of nephrocystin-1 (NPHP1) result in abnormal structure and function of the primary cilia. These deletions can result in a tubulointerstitial kidney disease known as nephronophthisis and retinal (Senior–Løken syndrome) and neurological (Joubert syndrome) diseases. Nephronophthisis is a common cause of end-stage kidney disease (ESKD) in children and up to 1% of adult onset ESKD. Single nucleotide variants (SNVs) and small insertions and deletions (Indels) have been less well characterised. We used a gene pathogenicity scoring system (GenePy) and a genotype-to-phenotype approach on individuals recruited to the UK Genomics England (GEL) 100,000 Genomes Project (100kGP) (n = 78,050). This approach identified all participants with NPHP1-related diseases reported by NHS Genomics Medical Centres and an additional eight participants. Extreme NPHP1 gene scores, often underpinned by clear recessive inheritance, were observed in patients from diverse recruitment categories, including cancer, suggesting the possibility of a more widespread disease than previously appreciated. In total, ten participants had homozygous CNV deletions with eight homozygous or compound heterozygous with SNVs. Our data also reveals strong in-silico evidence that approximately 44% of NPHP1 related disease may be due to SNVs with AlphaFold structural modelling evidence for a significant impact on protein structure. This study suggests historical under-reporting of SNVS in NPHP1 related diseases compared with CNVs.