Indel Variants Research Articles

Bioinformatics pipeline to guide post‐GWAS studies in Alzheimer’s: a new catalogue of disease candidate short structural variants

AbstractBackgroundShort structural variants (SSVs) including indels are common in the human genome and impact disease risk. The role of SSVs in late onset Alzheimer’s disease (LOAD) has been understudied. Previously we developed a bioinformatics pipeline that characterizes and prioritizes candidate regulatory SNPs in enhancers located in LOAD‐GWAS regions. Here we developed a bioinformatics pipeline of SSVs within LOAD‐GWAS regions to prioritize regulatory SSVs based on the strength of their predicted effect on transcription factor (TFs) binding sites. The impact of the genes and TFs prioritized by the pipeline are assessed in two LOAD single cell rna‐seq datasets.MethodsThe pipeline utilized publicly available functional genomics data sources. Primarily, candidate cis‐regulatory elements (cCREs) from ENCODE and publicly available single‐cell RNA‐seq data from LOAD patient samples from human prefrontal cortex brain samples obtained from UCI MIND’s Alzheimer’s Disease Research Center (ADRC) and ROSMAP. For TF binding analysis we employed motifs from MotifDb. In addition, we used various bioinformatics software including motifbreakR.ResultsWe catalogued 1230 proximal CTCF‐bound candidate cis‐regulatory elements in LOAD‐GWAS regions, 912 showed epigenetic evidence in relevant brain tissue. We catalogued 426 indels in these cCREs. These indels disrupted 391 TFs, 362 of these had snRNA‐seq data from LOAD samples. Of note, TF motifs within the APOE‐TOMM40, SPI1 and MS4A2 regions were significantly disrupted by the candidate regulatory indels. Amongst these TFs are RUNX3, SPI1 and SMAD3. Interestingly, these significant findings with the APOE‐TOMM40, SPI1 and MS4A2 regions are consistent with our prior results for SNPs.ConclusionsThis study provides an analytical framework to catalogue noncoding indel variation in cis‐regulatory elements located in LOAD‐GWAS loci and characterize their likelihood to perturb TF binding. The approach integrates multiple data types to prioritize genes and variants for validation experiments using disease models and gene editing technologies.

Screening of Fast-Neutron Mutant Population to Identify Candidate Rice Blast Defense Response Genes

Rice is the most widely consumed staple food in the world, feeding over half of global population. Thailand has long been an important rice producer and exporter, ranked 6th in the world regarding total milled rice yield. Unfortunately, the major problem of rice production worldwide is rice blast disease which caused by the fungus Magnaporthe oryzae. The most effective method for managing rice blast disease is using resistant rice varieties. One of Thai rice variety that show highly resistance against various rice blast fungus isolates is Jao Hom Nin (JHN) rice, containing broad-spectrum resistance gene, Pi7. However, the identification of resistance genes other than the R gene will confer long-lasting and sustainable resistance to the plant, which lead to identification of genes involved in the plant’s defense against the rice blast fungus in this study. JHN were previously mutagenized with fast-neutron radiation. 2,200 JHN M4 lines were inoculated with mixture of five Thai rice blast fungus isolates. Five susceptible lines lost their resistance due to mutations in the Pi7 gene, while one susceptible line with an intact Pi7 gene could not be characterized as it failed to produce an F1 population. Two moderate resistance lines with intact Pi7 gene were sent for whole-genome resequencing along with JHN wildtype. The sequence comparison between JHN and two mutant lines revealed 491,759 Indel variants. The Indel variants, whose nucleotide sequences differed by less than 10 bp between JHN and mutants, were filtered out. Consequently 33 candidate rice blast defense response genes were predicted to contain high-impact effect Indels, with only 15 of them having predicted functions. Eleven genes were identified as transposons or retrotransposons. Four genes with predicted functions stand out as interesting candidates for future characterization.

Adult Onset of Pyruvate Dehydrogenase Deficiency Presenting with Dystonia and Chorea in Female Patient from India - A Very Rare Case

We reported a very rare case of pyruvate dehydrogenase complex E1α (PDHA1) gene deficiency presenting as cervical dystonia and chorea in an adult female patient from India. Patient was presented with a history of involuntary rhythmic repetitive movements of both hands, legs, and head, lips and stammering of speech with tilting of neck to one side along with orofacial dyskinetic movements since past 6 years and gait changes since past 4 years. Her symptoms were progressive in nature. Her physical examination and systemic examinations were normal. Neurological examinations suggestive of cervical dystonia with chorea form movements. Brain MRI investigations revealed marked atrophy of bilateral caudate nuclei and putamina. Patient had a familial history of father and second brother had mild hand tremors. Patient has been referred for whole exome sequencing. The exome data analysis identified a very rare and unusual heterozygous indel variant c.-20_-19delinsCT, (chrX:19344018_19344019delinsCT) in 5’UTR region of PDHA1 gene caused late phenotypic onset of cervical dystonia as major clinical manifestation of PDHA1 deficiency along with chorea form movement disorders at the age of 24 year. In conclusion, to the best of our literature knowledge this is the novel and unusual case of adult female patient wherein we are reporting a novel heterozygous indel variant c.-20_-19delinsCT, (chrX:19344018_19344019delinsCT) in 5’UTR region of PDHA1 gene responsible for PDHA1 deficiency presenting with cervical dystonia and chorea as major clinical manifestations. Hence, dystonia and chorea as major clinical manifestations of PDH deficiency could be considered in adult patients also rather than only in paediatric patients.

A 1-bp deletion in the MC04g1399 is highly associated with failure to produce fruit wart in bitter gourd (Momordica charantia L.)

Fruit wart is an important appearance trait influencing consumer preferences of bitter gourd. The molecular genetic mechanisms underlying fruit wart formation in bitter gourd are largely unknown. In this study, genetic analysis based on four generations showed that fruit wart formation in bitter gourd was controlled by a single dominant locus named as Fwa. The Fwa locus was initially mapped into a 4.82 Mb region on pseudochromosome 4 by BSA-seq analysis and subsequently narrowed down to a 286.30 kb region by linkage analysis. A large F2 population consisting of 2 360 individuals was used to screen recombinants, and the Fwa locus was finally fine mapped into a 22.70 kb region harboring four protein-coding genes through recombination analysis. MC04g1399, encoding an epidermal patterning factor 2-like protein, was proposed as the best candidate gene for Fwa via sequence variation and expression analysis. In addition, a 1-bp insertion and deletion (InDel) variation within MC04g1399 was converted to a cleaved amplified polymorphic sequence (CAPS) marker that could precisely distinguish between the warty and non-warty types with an accuracy rate of 100 % among a wide panel of 126 bitter gourd germplasm resources. Our results not only provide a scientific basis for deciphering the molecular mechanisms underlying fruit wart formation but also provide a powerful tool for efficient genetic improvement of fruit wart via marker-assisted selection.

Exome Sequencing Identifies Multiple Genetic Diagnoses in Children with Syndromic Growth Disorders

To evaluate the presence of multiple genetic diagnoses in syndromic growth disorders. We carried out a cross-sectional study to evaluate 115 patients with syndromic tall (n=24) or short stature (n=91) of unknown cause from a tertiary referral center for growth disorders. Exome sequencing was performed to assess germline single nucleotide, InDel, and copy number variants. All variants were classified according to ACMG/AMP guidelines. The main outcome measured was the frequency of multiple genetic diagnoses in a cohort of children with syndromic growth disorders. The total diagnostic yield of the cohort was 54.8% (63/115). Six patients had multiple genetic diagnoses (tall stature group=2; short stature group=4). The proportion of multiple diagnoses within total cases was 5.2% (6/115), and within solved cases was 9.5% (6/63). No characteristics were significantly more frequent when compared with patients with single or multiple genetic findings. Among patients with multiple diagnoses, 3 had syndromes with overlapping clinical features, and the others had syndromes with distinct phenotypes. Recognition of multiple genetic diagnoses as a possibility in complex cases of syndromic growth disorders opens a new perspective on treatment and genetic counseling for affected patients, defying the medical common sense of trying to fit all findings into one diagnosis.

Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).

Background: Automating data analysis pipelines is a key requirement to ensure reproducibility of results, especially when dealing with large volumes of data. Here we assembled automated pipelines for the analysis of High-throughput Sequencing (HTS) data originating from RNA-Seq, ChIP-Seq and Germline variant calling experiments. We implemented these workflows in Common workflow language (CWL) and evaluated their performance by: i) reproducing the results of two previously published studies on Chronic Lymphocytic Leukemia (CLL), and ii) analyzing whole genome sequencing data from four Genome in a Bottle Consortium (GIAB) samples, comparing the detected variants against their respective golden standard truth sets. Findings: We demonstrated that CWL-implemented workflows clearly achieved high accuracy in reproducing previously published results, discovering significant biomarkers and detecting germline SNP and small INDEL variants. Conclusion: CWL pipelines are characterized by reproducibility and reusability; combined with containerization, they provide the ability to overcome issues of software incompatibility and laborious configuration requirements. In addition, they are flexible and can be used immediately or adapted to the specific needs of an experiment or study. The CWL-based workflows developed in this study, along with version information for all software tools, are publicly available on GitHub (https://github.com/BiodataAnalysisGroup/CWL_HTS_pipelines) under the MIT License. They are suitable for the analysis of short-read (such as Illumina-based) data and constitute an open resource that can facilitate automation, reproducibility and cross-platform compatibility for standard bioinformatic analyses.

A Functional Variant Alters the Binding of Bone morphogenetic protein 2 to the Transcription Factor NF-κB to Regulate Bone morphogenetic protein 2 Gene Expression and Chicken Abdominal Fat Deposition

In this study, we employed a dual-luciferase reporter assay and electrophoretic mobility shift analysis (EMSA) in vitro to explore whether a 12-base pair (bp) insertion/deletion (InDel) variant (namely g.14798187_14798188insTCCCTGCCCCCT) within intron 2 of the chicken BMP2 gene, which was significantly associated with chicken abdominal fat weight and abdominal fat percentage, is a functional marker and its potential regulatory mechanism. The reporter analysis demonstrated that the luciferase activity of the deletion allele was extremely significantly higher than that of the insertion allele (p < 0.01). A bioinformatics analysis revealed that compared to the deletion allele, the insertion allele created a transcription factor binding site of nuclear factor-kappa B (NF-κB), which exhibited an inhibitory effect on fat deposition. A dual-luciferase reporter assay demonstrated that the inhibitory effect of NF-κB on the deletion allele was stronger than that on the insertion allele. EMSA indicated that the binding affinity of NF-κB for the insertion allele was stronger than that for the deletion allele. In conclusion, the 12-bp InDel chicken BMP2 gene variant is a functional variant affecting fat deposition in chickens, which may partially regulate BMP2 gene expression by affecting the binding of transcription factor NF-κB to the BMP2 gene.

Multiplexed Functional Assessment of Glanzmann Thrombasthenia Variants

High throughput genome and exome sequencing tests are used to identify disease-causing genetic variants, including those that cause inherited platelet disorders (IPDs) like Glanzmann Thrombasthenia (GT). However, most variants identified in clinical tests are classified as variants of unknown significance (VUS), lacking sufficient evidence to guide informed clinical decision-making. This frequent result of a VUS complicates clinical diagnosis and can be a source of uncertainty, distress, and inequity for patients. Functional studies that demonstrate a damaging effect of variants are considered strong evidence of pathogenicity but are missing for most variants. However, individually testing the function of all possible missense changes in IPD genes is impractical. Multiplexed assays of variant effect (MAVEs) have been developed for select diseases to simultaneously measure the functional effect of all possible nucleotides in a specific genomic region. However, MAVEs have typically been employed in cell lines, and often utilize over-expression systems, which don't account for the proper cellular and genomic context needed to assess variants in IPDs. In this study, we use CRISPR/CAS9 mediated homology directed repair (HDR) in CD34+ cells to create MKs with GT mutations in the gene ITGA2B and show that they model GT patient platelet phenotypes. We then implement a MAVE in CD34+ derived MKs to evaluate the impact on αIIb expression of a library of all possible single nucleotide changes for 12 nucleotides surrounding a type I GT variant. This was done by introducing a pooled library of HDR donors containing a mixture of test variants into CD34+ cells. This resulted in a pool of endogenously edited MKs, each containing one of 32 different nucleotide changes. These MKs were sorted into CD42+ and CD41+ or CD41- populations and analyzed using high throughput sequencing to assess variant enrichment. Analysis of sequencing reads indicated distribution of variant containing reads across all 12 nucleotides and incorporation of all 48 different HDR donors (32 changes, 12 identity replacements). Numerous indels were also identified. Our results identified two distinct clusters of variants: those supporting a damaging effect on expression, and those likely having no effect on expression. Notably, we observed that all nonsense variants and indels resulting in a stop codon clustered in the CD41- enriched population, whereas all silent variants clustered in the CD41+ enriched population. To classify variants more precisely, we used an expectation-maximization (EM) algorithm based on the distribution of read counts between the CD41+ and CD41- populations. This identified 12 missense, 3 nonsense, and 30 indel variants as abnormal, compared to 24 missense and 10 silent variants as normal with respect to CD41 expression. Agreement of our results with computational assessments of variant effects supported the findings. In conclusion, we developed an approach for the multiplexed assessment of GT variants, enabling the simultaneous evaluation of the functional effect of at least 32 different variants within a specific region of ITGA2B. This opens the door to assessing the functional impact of all possible nucleotide changes across the entire ITGA2B coding region and lays the foundation for similar investigations in other IPD genes.

Neurodevelopmental and other phenotypes recurrently associated with heterozygous BAZ2B loss-of-function variants.

The bromodomain adjacent to zinc finger 2B (BAZ2B) gene encodes a chromatin remodeling protein that has been shown to perform a variety of regulatory functions. It has been proposed that loss of BAZ2B function is associated with neurodevelopmental phenotypes, and some recurrent structural birth defects and dysmorphic features have been documented among individuals carrying heterozygous loss-of-function BAZ2B variants. However, additional evidence is needed to confirm that these phenotypes are attributable to BAZ2B deficiency. Here, we report 10 unrelated individuals with heterozygous deletions, stop-gain, frameshift, missense, splice junction, indel, and start-loss variants affecting BAZ2B. These included a paternal intragenic deletion and a maternal frameshift variant that were inherited from mildly affected or asymptomatic parents. The analysis of molecular and clinical data from this cohort, and that of individuals previously reported, suggests that BAZ2B haploinsufficiency causes an autosomal dominant neurodevelopmental syndrome that is incompletely penetrant. The phenotypes most commonly seen in association with loss of BAZ2B function include developmental delay, intellectual disability, autism spectrum disorder, speech delay-with some affected individuals being non-verbal-behavioral abnormalities, seizures, vision-related issues, congenital heart defects, poor fetal growth, and an indistinct pattern of dysmorphic features in which epicanthal folds and small ears are particularly common.

A rapid, multiplex digital PCR assay to detect gene variants and fusions in non-small cell lung cancer.

Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation-based multiplex dPCR assay capable of detecting 12 single-nucleotide and insertion/deletion (indel) variants in EGFR, KRAS, BRAF, and ERBB2, 14 gene fusions in ALK, RET, ROS1 and NTRK1, and MET exon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target-signal encoding to improve the specificity of variant detection by reducing background noise by up to an order of magnitude. The assay reported an overall 100% positive percent agreement (PPA) and 98.5% negative percent agreement (NPA) compared to a sequencing-based assay in a cohort of 62 human formalin-fixed paraffin-embedded (FFPE) samples. In addition, the dPCR assay rescued actionable information in ten samples that failed to sequence, highlighting the utility of a multiplexed digital PCR assay as a potential reflex solution for challenging NSCLC samples.

Association of apoptosis-related variants to malaria infection and parasite density in individuals from the Brazilian Amazon

BackgroundIn malaria infection, apoptosis acts as an important immunomodulatory mechanism that leads to the elimination of parasitized cells, thus reducing the parasite density and controlling immune cell populations. Here, it was investigated the association of INDEL variants in apoptotic genes—rs10562972 (FAS), rs4197 (FADD), rs3834129 and rs59308963 (CASP8), rs61079693 (CASP9), rs4647655 (CASP3), rs11269260 (BCL-2), and rs17880560 (TP53)—and the influence of genetic ancestry with susceptibility to malaria and parasite density in an admixed population from the Brazilian Amazon.MethodsTotal DNA was extracted from 126 malaria patients and 101 uninfected individuals for investigation of genetic ancestries and genotypic distribution of apoptosis-related variants by Multiplex PCR. Association analyses consisted of multivariate logistic regressions, considering the following comparisons: (i) DEL/DEL genotype vs. INS/DEL + INS/INS; and (ii) INS/INS vs. INS/DEL + DEL/DEL.ResultsIndividuals infected by Plasmodium falciparum had significantly higher African ancestry proportions in comparison to uninfected controls, Plasmodium vivax, and mixed infections. The INS/INS genotype of rs3834129 (CASP8) seemed to increase the risk for P. falciparum infection (P = 0.038; OR = 1.867; 95% CI 0.736–3.725), while the DEL/DEL genotype presented a significant protective effect against infection by P. falciparum (P = 0.049; OR = 0.446; 95% CI 0.185–0.944) and mixed infection (P = 0.026; OR = 0.545; 95% CI 0.281–0.996), and was associated with lower parasite density in P. falciparum malaria (P = 0.009; OR = 0.383; 95% CI 0.113–1.295). Additionally, the INS/INS genotype of rs10562972 (FAS) was more frequent among individuals infected with P. vivax compared to P. falciparum (P = 0.036; OR = 2.493; 95% CI 1.104–4.551), and the DEL/DEL genotype of rs17880560 (TP53) was significantly more present in patients with mono-infection by P. vivax than in individuals with mixed infection (P = 0.029; OR = 0.667; 95% CI 0.211–1.669).ConclusionsIn conclusion, variants in apoptosis genes are associated with malaria susceptibility and parasite density, indicating the role of apoptosis-related genetic profiles in immune responses against malaria infection.

Identification of Late Ripening Citrus Mutant, Ara-unshiu (Citrus unshiu), and Its Selectable Marker.

'Miyagawa-wase' mandarin (Citrus unshiu Marc. cv. Miyagawa-wase early) is one of the most widely cultivated citrus varieties on Jeju Island in Korea. Mutation breeding is a useful tool for the induction of genetic diversity for the rapid creation of new plant variants. We previously reported the use of gamma irradiation for the development of new citrus varieties. Here, we report a new mutant, Ara-unshiu, with a unique late fruit ripening phenotype. We investigated the fruit morphological characteristics including weight, vertical/transverse diameter, peel thickness, hardness, and color difference, as well as sugar and acid contents of the Ara-unshiu compared to wild-type controls. We then used whole genome re-sequencing and functional annotation by gene ontology to identify and characterize single nucleotide polymorphism (SNP) and insertion/deletion (InDel) variants in the Ara-unshiu, finding a greater abundance of annotated genes containing InDels compared to SNPs. Finally, we used allele-specific PCR to identify molecular markers among the homozygous SNPs detected from the Ara-unshiu genome sequencing. We report a primer set that effectively distinguishes the Ara-unshiu from the wild-type control and other citrus varieties. Our findings provide insights into the mechanisms controlling the timing of fruit ripening and tools for the molecular breeding of citrus varieties.

Functional allele of a MATE gene selected during domestication modulates seed color in chickpea.

Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.

Insight into the drug-resistant characteristics and genetic diversity of multidrug-resistant Mycobacterium tuberculosis in China.

Multidrug-resistant tuberculosis (MDR-TB) has a severe impact on public health. To investigate the drug-resistant profile, compensatory mutations and genetic variations among MDR-TB isolates, a total of 546 MDR-TB isolates from China underwent drug-susceptibility testing and whole genome sequencing for further analysis. The results showed that our isolates have a high rate of fluoroquinolone resistance (45.60%, 249/546) and a low proportion of conferring resistance to bedaquiline, clofazimine, linezolid, and delamanid. The majority of MDR-TB isolates (77.66%, 424/546) belong to Lineage 2.2.1, followed by Lineage 4.5 (6.41%, 35/546), and the Lineage 2 isolates have a strong association with pre-XDR/XDR-TB (P < 0.05) in our study. Epidemic success analysis using time-scaled haplotypic density (THD) showed that clustered isolates outperformed non-clustered isolates. Compensatory mutations happened in rpoA, rpoC, and non-RRDR of rpoB genes, which were found more frequently in clusters and were associated with the increase of THD index, suggesting that increased bacterial fitness was associated with MDR-TB transmission. In addition, the variants in resistance associated genes in MDR isolates are mainly focused on single nucleotide polymorphism mutations, and only a few genes have indel variants, such as katG, ethA. We also found some genes underwent indel variation correlated with the lineage and sub-lineage of isolates, suggesting the selective evolution of different lineage isolates. Thus, this analysis of the characterization and genetic diversity of MDR isolates would be helpful in developing effective strategies for treatment regimens and tailoring public interventions. IMPORTANCE Multidrug-resistant tuberculosis (MDR-TB) is a serious obstacle to tuberculosis prevention and control in China. This study provides insight into the drug-resistant characteristics of MDR combined with phenotypic drug-susceptibility testing and whole genome sequencing. The compensatory mutations and epidemic success analysis were analyzed by time-scaled haplotypic density (THD) method, suggesting clustered isolates and compensatory mutations are associated with MDR-TB transmission. In addition, the insertion and deletion variants happened in some genes, which are associated with the lineage and sub-lineage of isolates, such as the mpt64 gene. This study offered a valuable reference and increased understanding of MDR-TB in China, which could be crucial for achieving the objective of precision medicine in the prevention and treatment of MDR-TB.

PredinID: Predicting Pathogenic Inframe Indels in Human Through Graph Convolution Neural Network With Graph Sampling Technique.

Inframe insertion/deletion (indel) variants may alter protein sequence and function, which are closely related to an extensive variety of diseases. Although recent researches have paid attention to the associations between inframe indels and diseases, modeling indels in silico and interpreting their pathogenicity remain challenging, mainly due to the lack of experimental information and computational methodologies. In this article, we propose a novel computational method named PredinID (Predictor for inframe InDels) via graph convolutional network (GCN). PredinID leverages k-nearest neighbor algorithm to construct the feature graph for aggregating more informative representation, regarding the pathogenic inframe indel prediction as a node classification task. An edge-based sampling strategy is designed for extracting information from both the potential connections of feature space and the topological structure of subgraphs. Evaluated by 5-fold cross-validations, the PredinID method achieves satisfactory performance and is superior to four classic machine learning algorithms and two GCN methods. Comprehensive experiments show that PredinID has superior performances when compared with the state-of-the-art methods on the independent test set. Moreover, we also implement a web server at http://predinid.bio.aielab.cc/, to facilitate the use of the model.

HLA-G*14 bp indel variant in autism spectrum disorder in a population from southern Brazil

Altered immune response during pregnancy has been associated with ASD susceptibility. HLA-G is expressed by the trophoblast at the maternal/fetal interface and induces allogenic tolerance toward the fetus. A 14-bp insertion in the HLA-G 3’UTR (rs371194629) was associated with reduced levels of HLA-G. We aimed to assess the influence of the HLA-G*14 bp indel variant in ASD susceptibility and symptomatology in a Brazilian admixed sample. The insertion genotype (14 bp+/14 bp+) was firstly associated with hetero aggression, but statistical significance was lost after correction (p = 0.035, pcorrected = 0.35). No association between the HLA-G variant and susceptibility to ASD or differential clinical manifestations were observed.

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.

The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. We report the analysis of > 48M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

Confirmation of Insertion, Deletion, and Deletion-Insertion Variants Detected by Next-Generation Sequencing.

Despite clinically demonstrated accuracy in next generation sequencing (NGS) data, many clinical laboratories continue to confirm variants with Sanger sequencing, which increases cost of testing and turnaround time. Several studies have assessed the accuracy of NGS in detecting single nucleotide variants; however, less has been reported about insertion, deletion, and deletion-insertion variants (indels). We performed a retrospective analysis from 2015-2022 of indel results from a subset of NGS targeted gene panel tests offered through the Mayo Clinic Genomics Laboratories. We compared results from NGS and Sanger sequencing of indels observed in clinical runs and during the intra-assay validation of the tests. Results demonstrated 100% concordance between NGS and Sanger sequencing for over 490 indels (217 unique), ranging in size from 1 to 68 basepairs (bp). The majority of indels were deletions (77%) and 1 to 5 bp in length (90%). Variant frequencies ranged from 11.4% to 67.4% and 85.1% to 100% for heterozygous and homozygous variants, respectively, with a median depth of coverage of 2562×. A subset of indels (7%) were located in complex regions of the genome, and these were accurately detected by NGS. We also demonstrated 100% reproducibility of indel detection (n = 179) during intra-assay validation. Together this data demonstrates that reportable indel variants up to 68 bp can be accurately assessed using NGS, even when they occur in complex regions. Depending on the complexity of the region or variant, Sanger sequence confirmation of indels is usually not necessary if the variants meet appropriate coverage and allele frequency thresholds.

Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.)

BackgroundSingle nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the most abundant genetic variations and widely distribute across the genomes in plant. Development of SNP and InDel markers is a valuable tool for genetics and genomic research in radish (Raphanus sativus L.).ResultsIn this study, a total of 366,679 single nucleotide polymorphisms (SNPs) and 97,973 insertion-deletion (InDel) markers were identified based on genome resequencing between ‘YZH’ and ‘XHT’. In all, 53,343 SNPs and 4,257 InDels were detected in two cultivars by transcriptome sequencing. Among the InDel variations, 85 genomic and 15 transcriptomic InDels were newly developed and validated PCR. The 100 polymorphic InDels markers generated 207 alleles among 200 Chinese radish germplasm, with an average 2.07 of the number of alleles (Na) and with an average 0.33 of the polymorphism information content (PIC). Population structure and phylogenetic relationship revealed that the radish cultivars from northern China were clustered together and the southwest China cultivars were clustered together. RNA-Seq analysis revealed that 11,003 differentially expressed genes (DEGs) were identified between the two cultivars, of which 5,020 were upregulated and 5,983 were downregulated. In total, 145 flowering time-related DGEs were detected, most of which were involved in flowering time integrator, circadian clock/photoperiod autonomous, and vernalization pathways. In flowering time-related DGEs region, 150 transcriptomic SNPs and 9 InDels were obtained.ConclusionsThe large amount of SNPs and InDels identified in this study will provide a valuable marker resource for radish genetic and genomic studies. The SNPs and InDels within flowering time-related DGEs provide fundamental insight into for dissecting molecular mechanism of bolting and flowering in radish.

The Role of Rora (Rar-Related Orphan Receptor Alpha) Receptors, One of The Candidate Genes Identified for Sheep Reproductive Traits, In Sheep Reproduction

RORA (RAR-Related Orphan Receptor Alpha) regulates estrogen synthesis by transcribing steroid related genes. Litter size is an important reproductive trait associated with estrogen synthesis. Therefore, it is critical to investigate the relationship between the RORA gene and sheep litter size. In this study, a 23 base pair nucleotide sequence mutation in a gene called RORA and the effect of this mutation on the productivity of sheep offspring were investigated. In this study, a 23 bp nucleotide sequence mutation was found in intron 1 of the RORA gene in 35 female Bafra ewes. Ten ml of milk was collected from each of the 35 samples. The litter size of the DD genotype was significantly higher than the ID genotype and the II genotype in the second born litter size (p&amp;gt; 0.05). The relationship between combined genotypes and average litter size showed that ewes with homozygous (DD) genotype had larger lambs than ewes with heterozygous (ID) genotype. Multiple pregnancy rates in the first and second litters were higher than the average stillbirth rate (p&amp;gt; 0.05). To summarize, this study provided theoretical references for further research on the function of RORA gene and breeding of Bafra sheep. The 23-bp indel variants can be used as molecular markers for the size of first and second born offspring of ewes in MAS (marker assisted selection) breeding.