Explore the vast range of titles available.

GNAS is a complex gene that encodes Gs[alpha], a signaling protein that triggers a complex network of pathways. Heterozygous inactivating mutations in Gs[alpha]-coding GNAS exons cause hormonal resistance; on the contrary, activating mutations in Gs[alpha] result in constitutive cAMP stimulation. Recent research has described a clinical condition characterized by both gain and loss of Gs[alpha] function, due to a heterozygous de novo variant of the maternal GNAS allele. We describe a girl with a complex combination of clinical signs and a new heterozygous GNAS variant. For the molecular analysis of GNAS gene, DNA samples of the proband and her parents were extracted from their peripheral blood samples. In silico analysis was performed to predict the possible in vivo effect of the detected novel genetic variant. The activity of Gs[alpha] protein was in vitro analyzed from samples of erythrocyte membranes, recovered from heparinized blood samples. We found a new heterozygous missense c.166A > T--(p.Ile56Phe) GNAS variant in exon 2, inherited from the mother that determined a reduced activity of 50% of Gs[alpha] protein function. The analysis of her parents showed a 20-25% reduction in Gs[alpha] protein activity in the mother and a normal function in the father. Clinically our patient presented a multisystemic disorder characterized by hyponatremia compatible with a nephrogenic syndrome of inappropriate antidiuresis, subclinical hyperthyroidism, subclinical hypercortisolism, precocious thelarche and pubarche and congenital bone abnormalities. This is the first time that the new variant c.166A > T (p.Ile56Phe) on exon 2 of GNAS gene, originated on maternal allele, has been described as probable cause of a multisystemic disorder. Although the mutation is associated with a reduced activity of the function of Gs[alpha] protein, this unusual phenotype on the contrary suggests a mild functional gain.

Background GNAS is a complex gene that encodes Gs[alpha], a signaling protein that triggers a complex network of pathways. Heterozygous inactivating mutations in Gs[alpha]-coding GNAS exons cause hormonal resistance; on the contrary, activating mutations in Gs[alpha] result in constitutive cAMP stimulation. Recent research has described a clinical condition characterized by both gain and loss of Gs[alpha] function, due to a heterozygous de novo variant of the maternal GNAS allele. Patients and methods We describe a girl with a complex combination of clinical signs and a new heterozygous GNAS variant. For the molecular analysis of GNAS gene, DNA samples of the proband and her parents were extracted from their peripheral blood samples. In silico analysis was performed to predict the possible in vivo effect of the detected novel genetic variant. The activity of Gs[alpha] protein was in vitro analyzed from samples of erythrocyte membranes, recovered from heparinized blood samples. Results We found a new heterozygous missense c.166A > T--(p.Ile56Phe) GNAS variant in exon 2, inherited from the mother that determined a reduced activity of 50% of Gs[alpha] protein function. The analysis of her parents showed a 20-25% reduction in Gs[alpha] protein activity in the mother and a normal function in the father. Clinically our patient presented a multisystemic disorder characterized by hyponatremia compatible with a nephrogenic syndrome of inappropriate antidiuresis, subclinical hyperthyroidism, subclinical hypercortisolism, precocious thelarche and pubarche and congenital bone abnormalities. Conclusions This is the first time that the new variant c.166A > T (p.Ile56Phe) on exon 2 of GNAS gene, originated on maternal allele, has been described as probable cause of a multisystemic disorder. Although the mutation is associated with a reduced activity of the function of Gs[alpha] protein, this unusual phenotype on the contrary suggests a mild functional gain. Keywords: GNAS gene, Hyponatremia, Subclinical hyperthyroidism, Precocious thelarche, Congenital bone abnormalities

In the present study, an [alpha]-thalassemia deletion [-[sup.SEA] (Southeast Asian)] and a compound heterozygote for the Chinese [sup.G][[gamma].sup.+][([sup.A][gamma][delta][beta]).sup.0]/[[beta].sup.CD17]- thalassemia mutation in a 15- year-old girl was identified by gap-PCR, PCR-reverse dot-blot hybridization and multiplex ligation-dependent probe amplification. Molecular analysis indicated that the proband's father carried a hemoglobin subunit p (HBB) heterozygous mutation in codon 17 (CD17; c.52A>T), the mother was a double hetero zygous carrier of the Chinese [sup.G][[gamma].sup.+][([sup.A][gamma][delta][beta]).sup.0]-thalassemia mutation combined with an -[sup.SEA] deletion, and the proband inherited both mutations from her mother and father, thus carrying the Chinese [sup.G][[gamma].sup.+][([sup.A][gamma][delta][beta]).sup.0]/[[beta].sup.CD17]- thalassemia combined with the- [sup.SEA] deletion in a compound heterozygous state. The proband was diagnosed as severe thalassemia intermedia and experienced a clinical phenotype aggravation (severe anemia and splenomegaly) from no obvious clinical symptoms to being dependent on monthly blood transfusions.

Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (F HOM ), uniting of gametes (F UNI ), and genotype additive variance (F GRM ) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (F ROH ). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

Inbreeding has long been recognized as a primary cause of fitness reduction in both wild and domesticated populations. Consanguineous matings cause inheritance of haplotypes that are identical by descent (IBD) and result in homozygous stretches along the genome of the offspring. Size and position of regions of homozygosity (ROHs) are expected to correlate with genomic features such as GC content and recombination rate, but also direction of selection. Thus, ROHs should be non-randomly distributed across the genome. Therefore, demographic history may not fully predict the effects of inbreeding. The porcine genome has a relatively heterogeneous distribution of recombination rate, making Sus scrofa an excellent model to study the influence of both recombination landscape and demography on genomic variation. This study utilizes next-generation sequencing data for the analysis of genomic ROH patterns, using a comparative sliding window approach. We present an in-depth study of genomic variation based on three different parameters: nucleotide diversity outside ROHs, the number of ROHs in the genome, and the average ROH size. We identified an abundance of ROHs in all genomes of multiple pigs from commercial breeds and wild populations from Eurasia. Size and number of ROHs are in agreement with known demography of the populations, with population bottlenecks highly increasing ROH occurrence. Nucleotide diversity outside ROHs is high in populations derived from a large ancient population, regardless of current population size. In addition, we show an unequal genomic ROH distribution, with strong correlations of ROH size and abundance with recombination rate and GC content. Global gene content does not correlate with ROH frequency, but some ROH hotspots do contain positive selected genes in commercial lines and wild populations. This study highlights the importance of the influence of demography and recombination on homozygosity in the genome to understand the effects of inbreeding.

In the present study, we report a human-inherited, impaired, adaptive immunity disorder, which predominantly manifested as a B cell differentiation defect, caused by a heterozygous IKZF3 missense variant, resulting in a glycine-to-arginine replacement within the DNA-binding domain of the encoded AIOLOS protein. Using mice that bear the corresponding variant and recapitulate the B and T cell phenotypes, we show that the mutant AIOLOS homodimers and AIOLOS–IKAROS heterodimers did not bind the canonical AIOLOS–IKAROS DNA sequence. In addition, homodimers and heterodimers containing one mutant AIOLOS bound to genomic regions lacking both canonical motifs. However, the removal of the dimerization capacity from mutant AIOLOS restored B cell development. Hence, the adaptive immunity defect is caused by the AIOLOS variant hijacking IKAROS function. Heterodimeric interference is a new mechanism of autosomal dominance that causes inborn errors of immunity by impairing protein function via the mutation of its heterodimeric partner. The zinc-finger transcription factor IKAROS is essential for B cell development. Taniuchi, Morio and colleagues identify a human kindred presenting with B cell immunodeficiency that was caused by a heterozygous missense mutation in IKZF3 encoding the related AIOLOS protein. AIOLOS G159R is a mutant protein that interferes with both wild-type AIOLOS and IKAROS by forming heterodimers that bind to aberrant DNA-binding sites and prevent normal expression of IKAROS-dependent genes.

Background: Ellis–van Creveld syndrome (EvCS) is an autosomal recessive ciliopathy with a disproportionate short stature, polydactyly, dystrophic nails, oral defects, and cardiac anomalies. It is caused by pathogenic variants in the EVC or EVC2 genes. To obtain further insight into the genetics of EvCS, we identified the genetic defect for the EVC2 gene in two Mexican patients. Methods: Two Mexican families were enrolled in this study. Exome sequencing was applied in the probands to screen potential genetic variant(s), and then Sanger sequencing was used to identify the variant in the parents. Finally, a prediction of the three-dimensional structure of the mutant proteins was made. Results: One patient has a compound heterozygous EVC2 mutation: a novel heterozygous variant c.519_519 + 1delinsT inherited from her mother, and a heterozygous variant c.2161delC (p.L721fs) inherited from her father. The second patient has a previously reported compound heterozygous EVC2 mutation: nonsense mutation c.645G > A (p.W215*) in exon 5 inherited from her mother, and c.273dup (p.K92fs) in exon 2 inherited from her father. In both cases, the diagnostic was Ellis–van Creveld syndrome. Three-dimensional modeling of the EVC2 protein showed that truncated proteins are produced in both patients due to the generation of premature stop codons. Conclusion: The identified novel heterozygous EVC2 variants, c.2161delC and c.519_519 + 1delinsT, were responsible for the Ellis–van Creveld syndrome in one of the Mexican patients. In the second Mexican patient, we identified a compound heterozygous variant, c.645G > A and c.273dup, responsible for EvCS. The findings in this study extend the EVC2 mutation spectrum and may provide new insights into the EVC2 causation and diagnosis with implications for genetic counseling and clinical management.

KLOTHO-VS heterozygosity (KL-VS[sup.het+] ) promotes longevity and protects against cognitive decline in aging. To determine whether KL-VS[sup.het+] mitigates Alzheimer’s disease (AD) progression, we used longitudinal linear-mixed models to compare the rate of change in multiple cognitive measures in AD patients stratified by APOE ε4 carrier status. We aggregated data on 665 participants (208 KL-VS[sup.het−] /ε4−, 307 KL-VS[sup.het−] /ε4+, 66 KL-VS[sup.het+] /ε4−, and 84 KL-VS[sup.het+] /ε4+) from two prospective cohorts, the National Alzheimer’s Coordinating Center and the Alzheimer’s Disease Neuroimaging Initiative. All participants were initially diagnosed with mild cognitive impairment, later developed AD dementia during the study, and had at least three subsequent visits. KL-VS[sup.het+] conferred slower cognitive decline in ε4 non-carriers (+0.287 MMSE points/year, p = 0.001; −0.104 CDR-SB points/year, p = 0.026; −0.042 ADCOMS points/year, p < 0.001) but not in ε4 carriers who generally had faster rates of decline than non-carriers. Stratified analyses showed that the protective effect of KL-VS[sup.het+] was particularly prominent in male participants, those who were older than the median baseline age of 76 years, or those who had an education level of at least 16 years. For the first time, our study provides evidence that KL-VS[sup.het+] status has a protective effect on AD progression and interacts with the ε4 allele.

Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the dl-49 chrX inversion in D . melanogaster . We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs outside of the proximal inversion breakpoint are distributed in a distance-dependent manner, with strongest suppression near the inversion breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, are not suppressed near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break formation. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.

Background Accurate structural variant detection from short-read sequencing data remains challenged by false positives, particularly for heterozygous deletions where reduced allelic support and coverage-based detection methods are ambiguous. Existing SV genotyping and filtering approaches suffer from significant recall reductions, dependencies on additional pre-computed resources, or restriction to depth-based signals that overlook read level evidence. Results Here we present SVhet, a novel computational framework that leverages the heterozygosity patterns detected from different read evidences to identify false heterozygous deletions. Comprehensive benchmarking using 31 Human Genome Structural Variation Consortium Phase 3 samples demonstrated SVhet's ability to further reduce false positives while maintaining baseline recall. Hybrid approach of duphold and SVhet achieved up to 60% reduction in false positive counts while preserving recall. We also showed SVhet to be computationally efficient that can complete a whole genome structural variant callset under 5 min using 4 CPU cores. SVhet is available under a permissive MIT license via https://github.com/snakesch/SVhet . Conclusion SVhet provides an accurate and efficient solution for evaluating heterozygous deletions derived from short read sequencing data. SVhet can be used as a standalone tool or in conjunction with other filtering tools such as duphold. Importantly, it does not require additional variant sets, and can operate with minimal compute. Altogether, SVhet adds to the current effort to achieve accurate structural variant detection using short reads.