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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.

Human nude SCID is a rare autosomal recessive inborn error of immunity (IEI) characterized by congenital athymia, alopecia, and nail dystrophy. Few cases have been reported to date. However, the recent introduction of newborn screening for IEIs and high-throughput sequencing has led to the identification of novel and atypical cases. Moreover, immunological alterations have been recently described in patients carrying heterozygous mutations. The aim of this paper is to describe the extended phenotype associated with FOXN1 homozygous, compound heterozygous, or heterozygous mutations. We collected clinical and laboratory information of a cohort of 11 homozygous, 2 compound heterozygous, and 5 heterozygous patients with recurrent severe infections. All, except one heterozygous patient, had signs of CID or SCID. Nail dystrophy and alopecia, that represent the hallmarks of the syndrome, were not always present, while almost 50% of the patients developed Omenn syndrome. One patient with hypomorphic compound heterozygous mutations had a late-onset atypical phenotype. A SCID-like phenotype was observed in 4 heterozygous patients coming from the same family. A spectrum of clinical manifestations may be associated with different mutations. The severity of the clinical phenotype likely depends on the amount of residual activity of the gene product, as previously observed for other SCID-related genes. The severity of the manifestations in this heterozygous family may suggest a mechanism of negative dominance of the specific mutation or the presence of additional mutations in noncoding regions.

CRISPR/Cas9 has become a powerful genome-editing tool for introducing genetic changes into crop species. In order to develop capacity for CRISPR/Cas9 technology in the tropical staple cassava ( ), the ( ) gene was targeted in two cultivars using constructs carrying gRNAs targeting two sequences within exon 13. After -mediated delivery of CRISPR/Cas9 reagents into cassava cells, both constructs induced visible albino phenotypes within cotyledon-stage somatic embryos regenerating on selection medium and the plants regenerated therefrom. A total of 58 (cv. 60444) and 25 (cv. TME 204) plant lines were recovered, of which 38 plant lines (19 from each cultivar) were analyzed for mutagenesis. The frequency of plant lines showing albino phenotype was high, ranging from 90 to 100% in cv. TME 204. Observed albino phenotypes were comprised of full albinos devoid of green tissue and chimeras containing a mixture of white and green tissues. Sequence analysis revealed that 38/38 (100%) of the plant lines examined carried mutations at the targeted site, with insertions, deletions, and substitutions recorded. One putatively mono-allelic homozygous line (1/19) was found from cv. 60444, while 1 (1/19) and 4 (4/19) putatively bi-allelic homozygous lines were found in 60444 and TME204, respectively. The remaining plant lines, comprised mostly of the chimeras, were found to be putatively heterozygous. We observed minor (1 bp) nucleotide substitutions and or deletions upstream of the 5' and or downstream of the 3' targeted region. The data reported demonstrates that CRISPR/Cas9-mediated genome editing of cassava is highly efficient and relatively simple, generating multi-allelic mutations in both cultivars studied. Modification of described here generates visually detectable mutated events in a relatively short time frame of 6-8 weeks, and does not require sequencing to confirm editing at the target. It therefore provides a valuable platform to facilitate rapid assessment and optimization of CRISPR/Cas9 and other genome-editing technologies in cassava.

Hypertriglyceridaemia is a very rare disorder caused by the mutations of LPL gene, with an autosomal recessive mode of inheritance. Here, we identified two unrelated Chinese patients manifested with severe hypertriglyceridaemia and acute pancreatitis. The clinical symptoms of proband 1 are more severe than proband 2. Whole exome sequencing and Sanger sequencing were performed. Functional analysis of the identified mutations has been done. Whole exome sequencing identified two pairs of variants in LPL gene in the proband 1 (c.162C>A and c.1322+1G>A) and proband 2 (c.835C>G and c.1322+1G>A). The substitution (c.162C>A) leads to the formation of a truncated (p.Cys54*) LPL protein. The substitution (c.835C>G) leads to the replacement of leucine to valine (p.Leu279Val). The splice donor site mutation (c.1322+1G>A) leads to the formation of alternative transcripts with the loss of 134 bp in exon 8 of the LPL gene. The proband 1 and his younger son also harbouring a heterozygous variant (c.553G>T; p.Gly185Cys) in APOA5 gene. The relative expression level of the mutated LPL mRNA (c.162C>A, c.835C>G and c.1322+1G>A) showed significant differences compared to wild‐type LPL mRNA, suggesting that all these three mutations affect the transcription of LPL mRNA. These three mutations (c.162C>A, c.835C>G and c.1322+1G>A) showed noticeably decreased LPL activity in cell culture medium but not in cell lysates. Here, we identified three mutations in LPL gene which causes severe hypertriglyceridaemia with acute pancreatitis in Chinese patients. We also described the significance of whole exome sequencing for identifying the candidate gene and disease‐causing mutation in patients with severe hypertriglyceridaemia and acute pancreatitis.

Objective: The objective of this study was to analyze the sequence of different fragments of the thyroperoxidase (TPO) gene from a cat diagnosed with congenital hypothyroidism (CH). Materials and Methods: The feline was diagnosed due to high serum concentrations of thy¬roid-stimulating hormone and low T4. The analysis of sequences containing mutations in the TPO gene from dogs with CH allowed for the prediction of mutation sites within the gene in an affected cat. In addition, the design of a polymerase chain reaction-based test allowed the amplification and sequencing of these gene segments. In addition, after the death of the patient, a necropsy and histopathology were performed, looking for macroscopic and microscopic alterations of affected organs. Results: The necropsy examination showed megacolon, cardiac concentric left ventricular hyper¬trophy, and bilateral enlargement of the thyroid gland. The histopathology of the thyroid showed follicular hypoplasia and low colloid production. gDNA analysis allowed the detection of mutation in the TPO gene, which corresponded to one transition in the nucleotide 12.542 (A > G) and het¬erozygous variations located in the nucleotide 14.627 (G/A) and in the nucleotide 30.713 (G/C). Conclusion: Due to the presence of these polymorphisms, it is suspected that one monoallelic expression of mutant alleles is present. More studies that allow an understanding of the role of the heterozygous in this pathology are required, as well as the role of gene mutations related to CH in cats. On the other hand, the data from the present study serve as the base for the development of a molecular test that allows a fast and accurate diagnosis of HC in cats.

Background Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops. Results Here, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape. Conclusions Thus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.

Advances in high-throughput sequencing techniques now allow relatively easy and affordable sequencing of large portions of the genome, even for nonmodel organisms. Many phylogenetic studies reduce costs by focusing their sequencing efforts on a selected set of targeted loci, commonly enriched using sequence capture. The advantage of this approach is that it recovers a consistent set of loci, each with high sequencing depth, which leads to more confidence in the assembly of target sequences. High sequencing depth can also be used to identify phylogenetically informative allelic variation within sequenced individuals, but allele sequences are infrequently assembled in phylogenetic studies. Instead, many scientists perform their phylogenetic analyses using contig sequences which result from the de novo assembly of sequencing reads into contigs containing only canonical nucleobases, and this may reduce both statistical power and phylogenetic accuracy. Here, we develop an easy-to-use pipeline to recover allele sequences from sequence capture data, and we use simulated and empirical data to demonstrate the utility of integrating these allele sequences to analyses performed under the multispecies coalescent model. Our empirical analyses of ultraconserved element locus data collected from the South American hummingbird genus Topaza demonstrate that phased allele sequences carry sufficient phylogenetic information to infer the genetic structure, lineage divergence, and biogeographic history of a genus that diversified during the last 3 myr. The phylogenetic results support the recognition of two species and suggest a high rate of gene flow across large distances of rainforest habitats but rare admixture across the Amazon River. Our simulations provide evidence that analyzing allele sequences leads to more accurate estimates of tree topology and divergence times than the more common approach of using contig sequences.

Oxidative agents can cause acute haemolytic anaemia in persons with G6PD deficiency. Understanding the relationship between G6PD genotype and the phenotypic expression of the enzyme deficiency is necessary so that severe haemolysis can be avoided. The patterns of oxidative haemolysis have been well described in G6PD deficient hemizygous males and homozygous females; and haemolysis in the proportionally more numerous heterozygous females has been documented mainly following consumption of fava beans and more recently dapsone. It has long been known that 8-aminoquinolines, notably primaquine and tafenoquine, cause acute haemolysis in G6PD deficiency. To support wider use of primaquine in Plasmodium vivax elimination, more data are needed on the haemolytic consequences of 8-aminoquinolines in G6PD heterozygous females. Two recent studies (in 2017) have provided precisely such data; and the need has emerged for the development of point of care quantitative testing of G6PD activity. Another priority is exploring alternative 8-aminoquinoline dosing regimens that are practical and improve safety in G6PD deficient individuals.

Glucagon-like peptide-1 (GLP-1) agonists are widely used in the management of type 2 diabetes and obesity, with their therapeutic scope expanding to address cardiometabolic and cardiorenal conditions. However, their increasing use has been associated with potential adverse effects, including acute pancreatitis (AP). The exact prevalence of GLP-1 agonist-induced AP remains uncertain and reliable predictors for its onset have yet to be identified. We present 3 cases of class-associated predilection for GLP-1 analog-associated AP in patients with carrier states for hemochromatosis (HC) and cystic fibrosis. Case 1 is a heterozygous carrier for the C282Y HC pathogenic variant. Case 2 is a heterozygous carrier of the Delta F508 deletion of the cystic fibrosis transmembrane regulator (CFTR) gene. Case 3 is compound heterozygous carrier of a single CFTR intron 9 poly T allele pathogenic variant (5T/7T/8T), as well as a single pathogenic variant of the C282Y HC gene. Our observation suggests that carrier states for cystic fibrosis and HC may predispose individuals to GLP-1 agonist-associated AP. Genetic testing for these carrier states should be considered among patients with GLP-1 agonist-associated AP to provide more support and data for this as a potential true risk factor.

Key messageWe demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources.Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava’s nutritional and agronomic traits, as well as for illuminating aspects of cassava’s history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.