Genotyping Strategy Research Articles

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9.

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPR-Cas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterial-conjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both single-gene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPR-Cas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.

Effectiveness and Efficiency of a Voriconazole Preemptive Genotyping Strategy

Effectiveness and Efficiency of a Voriconazole Preemptive Genotyping Strategy

Genome-wide SNP discovery through genotyping by sequencing, population structure, and linkage disequilibrium in Brazilian peach breeding germplasm

Genotyping by sequencing (GBS) is a flexible and cost-effective strategy for genome-wide SNP discovery and high-throughput genotyping. Here, we employed the GBS approach to explore population structure, genetic variability, and patterns of linkage disequilibrium (LD) among 220 peach genotypes (Prunus persica), representative of the Brazilian breeding germplasm. This selected panel is mainly composed by locally adapted peaches developed in mild winter and high relative humidity conditions, and represents a worldwide reference of peach germplasm for low-chilling areas. A total of 93,353 SNP markers were discovered, and after filtering, 18,373 high-quality SNPs were used in analyses. Thirty-four percent of selected SNPs were located in genic regions and about 70% of these in the coding sequence. Principal coordinate analysis (PCoA) and Bayesian clustering (fastSTRUCTURE) successfully detected population genetic structure in our germplasm panel, supporting the identification of three main distinct subpopulations. The distribution of the genotypes within subpopulations reflected their fruit-related traits: melting and non-melting flesh cultivars. LD patterns revealed a medium LD level in peach, with the extent of LD highly dependent on the subpopulation and genome regions. The use of GBS-SNPs to perform genome-wide association studies (GWAS) was also exploited by using phenotypic information from five fruit quality traits. The observed significant SNP-trait associations were always in the regions previously predicted by linkage and association mapping analysis, providing valuable insights to incorporate the use of marker-assisted selection in the breeding program.

Differential responses of antioxidant system and expression profile of some genes of two rice genotypes in response to salinity stress

Sketching an appropriate genotyping strategy needs a comprehensive understanding of plant endurance under stress. This study was performed to investigate the physiological and molecular responses of two rice genotypes (Hashemi parental and Hashemi advanced mutant line) with different sensitivity to salinity stress. Twenty five-day-old seedlings were treated with 0 (as control), 5 and 10 dS/m of NaCl and their characteristics corresponding to antioxidant enzymes were evaluated three times including 6 h, 48 h and 1 w after salinity treatment. The results showed that salinity stress significantly enhanced the cell oxidation levels [as thiobarbituric acid reactive substances (TBARS) content and lipoxygenase (LOX) activity] as well as antioxidant enzymes activities [superoxide dismutase (SOD), catalase (CAT), peroxidase (POX) and glutathione reductase (GR)] and ascorbate content. Moreover, the relative expression of SOD, CAT, ascorbate peroxidase (APX) and Oryza sativa dehydration responsive element binding (OsDREB2) genes significantly increased in response to salinity stress. Hashemi advanced mutant line (as tolerant genotype) showed the highest antioxidant enzymes activities and relative genes expression compared with Hashemi parental (as sensitive genotype). It can be concluded that overexpression of SOD, CAT, APX and OsDREB2 genes could be applied to enhance tolerance to salt stress.

Concordance of Giardia duodenalis assemblages determined by different PCR methodologies in three observational studies in Cuba

Giardia duodenalis is one of the most important intestinal parasites globally, especially in children, and in Cuba is the leading cause of chronic paediatric diarrhoea in this population. G. duodenalis is composed of eight genetic groups (or assemblages), two of which (A and B) are apparently zoonotic, occurring in both humans and other animals. However, consensus on the most appropriate genotyping scheme for optimal characterization of G. duodenalis isolates is lacking. In this article we present the results of three descriptive observational studies conducted in Havana, Cuba between 2010 and 2013, with the aim of comparing the results from molecular (PCR) approaches targeting different genes in order to assign with confidence 224 isolates of G. duodenalis to the correct assemblages. In each sub-study, following DNA isolation by the phenol/chloroform/isoamyl alcohol extraction method, PCR targeting the triose phosphate isomerase (tpi) gene was used for molecular characterization, as well as one additional PCR-method targeting another gene or pair of genes. DNA amplification was obtained in 87%, 83%, and 80% in the three sub-studies. Although excellent agreement (kappa index = 1) was recorded between results from some pairs of genes, for other combinations only moderate or substantial agreement was achieved. These results highlight the importance of interpretation of genotyping data, especially when single genetic markers are used. From the results of our studies, PCR targeting a combination of the tpi gene and the intergenic spacer region of rDNA may be a useful approach for the molecular characterization of G. duodenalis isolates.

Comparison of Three Assays for Identification of IDH Mutations in AML

Introduction Isocitrate dehydrogenase (IDH) mutations are present in up to 20% of acute myeloid leukemia (AML) patients and lead to production of 2-hydroxyglutarate which promotes impaired differentiation and leukemic cell proliferation. Currently, there are two FDA-approved IDH inhibitors for the treatment of AML: enasidenib and ivosidenib. It is now imperative to establish timely testing so that patients can take advantage of these new therapies. Here we compared three different genotyping strategies to identify the most reliable and cost-effective way of picking up IDH1 and IDH2 mutations in AML. Methodology We have tested 60 AML patient samples across three different methods for detection of IDH1/2 mutations: (i) Capillary Electrophoresis-Single Strand Conformational Analysis (CE-SSCA) with Sanger sequencing, (ii) Next generation sequencing (NGS) myeloid capture panel (SureSeq myPanel, Oxford Gene Technology, OGT; UK) and (iii) multi-cancer NGS amplicon panel (QIAseq Targeted DNA Panel, Qiagen, Germany). The NGS capture assay is a 26 gene panel designed for myeloid-related genes while the NGS amplicon panel includes 33 genes associated with haematological and non-haematological malignancies (Figure 1). We have compared the techniques and assessed the quality of the results by measuring gene coverage, read depth across the panels, sensitivity and specificity per test, and performed a final valuation including some practical considerations: cost analysis, staff timings, ease of assay operation, turnaround times (TATs), ease of analysis and reporting as well as batch size limits. We initially tested 424 AML cases with CE-SSCA and have successfully transferred to amplicon panel testing (to date 200 cases). Results The results from the initial 60 cases were concordant between both NGS technologies and Sanger sequencing. In total across all 3 assays, we have detected IDH mutations in 19% of the 624 samples tested (Figure 2). Two samples showed false positive results by CE-SSCA, but these were identified by Sanger sequencing; therefore CE-SSCA alone is an inadequate test and all positive samples by CE-SSCA have to be confirmed by Sanger sequencing. Two samples showed IDH1 R132H mutation with variant allele frequency less than 10%, which was detected by all methods, however the Sanger sequencing trace was very small and could potentially have been missed. The gene minimum read depth for capture NGS was 682 and 677 for amplicon, and the gene mean depth was 1571 and 934 reads, respectively. We did not identify any new genetic variants in IDH1/2. The cost of reagents was higher for the NGS capture panel at $235 per patient compared to amplicon based at $86 per patient, with CE-SSCA/Sanger sequencing combined costing $50. The amplicon NGS allows processing of up to 96 samples per batch, allowing for high throughput testing, while capture NGS only allows for 16 samples to be processed. The library preparation time (Figure 1) is shorter for NGS amplicon (2 days; 12 hours staff time) compared to capture (3 days; 17 hours staff time), with both techniques taking longer to set-up when compared to CE-SSCA (2 hours) and Sanger sequencing (1 day; 6 hours staff time). Looking at assay operation, CE-SSCA and Sanger are the less complex assays allowing for laboratory accessibility, whereas although NGS amplicon was relatively straight forward, NGS capture was slightly more complex, lending itself to specialist laboratory setup. When looking at analysis, CE-SSCA was straightforward; however certain patterns that are very similar to positive controls can lead to false positives. Both NGS analysis were very straightforward, taking <5min per sample, while CE-SSCA/Sanger can take up to 10min per sample in more difficult cases. Importantly, NGS-based approaches incorporate other clinically-relevant genes whereas CE-SSCA is limited to IDH1/2 evaluation with additional testing being required for other targets. Conclusion: We have established a multi-cancer NGS amplicon assay for the detection of IDH mutations in AML patients. It reduces test costs for patients, improving testing efficiencies, allowing additional clinically-relevant genes to be analysed in parallel It has also helped streamline testing for different cancer types which can now all follow the same workflow and be automated thus improving TAT's contributing to better patient management. Acknowledgements: Celgene provided funding for this study. Disclosures Taussig: Celgene: Research Funding.

Platelet Phenotype Prediction from Whole Genome Sequencing in 621 Sickle Cell Disease Patients

Introduction: Patients with sickle cell disease (SCD) are at increased risk of alloimmunization. Platelet refractoriness is a serious known complication and often seen in SCD patients who are heavily transfused and/or in the bone marrow transplantation (BMT) setting. Next generation sequencing (NGS) is an emerging and promising genotyping strategy in the context of blood typing, due its high throughput and its ability to detect both known and novel variants in the patient and donor population. Here we describe an algorithm to predict common and rare human platelet antigens (HPA) from NGS data, and its validation through Sanger sequencing. Design/Methods: Whole genome sequencing (WGS) was performed on stored blood samples from 621 SCD patients enrolled in 2 IRB-approved clinical studies. Our open source software RyLAN (Red Cell and Lymphocyte Antigen prediction from NGS) was utilized to translate WGS data into predicted RBC and platelet phenotypes. The 29 genomic variants interpreted by RyLAN in 6 HPA genes were correlated with Sanger sequencing. Results: Our study cohort consisted of 621 SCD patients (485 HbSS, 21 HbSβ0, 29 HbSβ+, 84 HbSC, 1HbS O Arab, and 1 HbSD). The mean age was 34.3 years, and 46% were male. Previous red cell transfusions were recorded in 62% of patients, and 3% were documented as never transfused. RyLAN software was executed as a singularity container in multithreaded mode, completing analysis of all 621 .bam WGS files in 18 hours. RyLAN predicted 237 unique extended platelet phenotype combinations in this cohort, with an average read depth of 33 in genomic areas of interest. Predictions for 10 platelet antigens in 26 participants, including rare phenotypes like HPA-25bw+ and HPA-13bw+, were confirmed by bidirectional Sanger. Conclusions: We describe an efficient, open-source algorithm used to interpret 6 HPA genes from WGS in a large SCD cohort. WGS, in conjunction with the RyLAN algorithm, demonstrated 100% accuracy in predicting common and rare HPA genomic variants. Future studies are needed to refine WGS algorithms in SCD, and to examine the possible value of this technology in HPA alloantibody identification workups, optimal platelet product allocation, and donor recruitment. Disclosures No relevant conflicts of interest to declare.

Considerations for Maintaining Family Diversity in Commercially Mass-Spawned Penaeid Shrimp: A Case Study on Penaeus monodon.

Skewed family distributions are common in aquaculture species that are highly fecund, communally (mass) spawned, and/or communally reared. The magnitude of skews pose challenges for maintaining family-specific genetic diversity, as increased resources are required to detect individuals from underrepresented families, or reliably determine relative survival as a measure of family performance. There is limited understanding of family skews or changes in family proportion of communally reared shrimp under commercial rearing conditions and particularly how this may affect genotyping strategies to recover family performance data in breeding programs. In this study, three separate batches of shrimp, Penaeus monodon, were communally spawned and reared, and then sampled as larvae when ponds were stocked at 30 days of culture (DOC) and as juveniles from commercial ponds during harvest at 150 DOC. A total of 199 broodstock contributed to the 5,734 progeny that were genotyped with a custom multiplex single nucleotide polymorphism (SNP) panel, and family assignments were cross-referenced using two parentage assignment methods, CERVUS and COLONY. A total of 121 families were detected, with some families contributing up to 11% of progeny at 30 DOC and up to 18% of progeny at harvest. Significant changes were detected for 20% of families from 30 to 150 DOC, with up to a 9% change in relative contribution. Family skew data was applied in several models to determine the optimal sample size to detect families, along with the ability to detect changes in relative family contribution over time. Results showed that an order of magnitude increase in sampling was required to capture the lowest represented 25% of families, as well as significantly improve the accuracy to determine changes in family proportion from 30 to 150 DOC. Practical measures may be implemented at the hatchery to reduce family skews; a cost-effective measure may be to address the initial magnitude differences in viable progeny produced among families, by pooling equal quantities of hatched larvae from each family. This study demonstrates the relationships between skews in families under commercial conditions, the ability to accurately detect families, and the balance of sampling effort and genotyping cost in highly fecund species such as shrimp.

Pooled genotyping strategies for the rapid construction of genomic reference populations1.

The growing concern with the environment is making important for livestock producers to focus on selection for efficiency-related traits, which is a challenge for commercial cattle herds due to the lack of pedigree information. To explore a cost-effective opportunity for genomic evaluations of commercial herds, this study compared the accuracy of bulls' genomic estimated breeding values (GEBV) using different pooled genotype strategies. We used ten replicates of previously simulated genomic and phenotypic data for one low (t1) and one moderate (t2) heritability trait of 200 sires and 2,200 progeny. Sire's GEBV were calculated using a univariate mixed model, with a hybrid genomic relationship matrix (h-GRM) relating sires to: 1) 1,100 pools of 2 animals; 2) 440 pools of 5 animals; 3) 220 pools of 10 animals; 4) 110 pools of 20 animals; 5) 88 pools of 25 animals; 6) 44 pools of 50 animals; and 7) 22 pools of 100 animals. Pooling criteria were: at random, grouped sorting by t1, grouped sorting by t2, and grouped sorting by a combination of t1 and t2. The same criteria were used to select 110, 220, 440, and 1,100 individual genotypes for GEBV calculation to compare GEBV accuracy using the same number of individual genotypes and pools. Although the best accuracy was achieved for a given trait when pools were grouped based on that same trait (t1: 0.50-0.56, t2: 0.66-0.77), pooling by one trait impacted negatively on the accuracy of GEBV for the other trait (t1: 0.25-0.46, t2: 0.29-0.71). Therefore, the combined measure may be a feasible alternative to use the same pools to calculate GEBVs for both traits (t1: 0.45-0.57, t2: 0.62-0.76). Pools of 10 individuals were identified as representing a good compromise between loss of accuracy (~10%-15%) and cost savings (~90%) from genotype assays. In addition, we demonstrated that in more than 90% of the simulations, pools present higher sires' GEBV accuracy than individual genotypes when the number of genotype assays is limited (i.e., 110 or 220) and animals are assigned to pools based on phenotype. Pools assigned at random presented the poorest results (t1: 0.07-0.45, t2: 0.14-0.70). In conclusion, pooling by phenotype is the best approach to implementing genomic evaluation using commercial herd data, particularly when pools of 10 individuals are evaluated. While combining phenotypes seems a promising strategy to allow more flexibility to the estimates made using pools, more studies are necessary in this regard.

The genetic landscape of the human solute carrier (SLC) transporter superfamily

The human solute carrier (SLC) superfamily of transporters is comprised of over 400 membrane-bound proteins, and plays essential roles in a multitude of physiological and pharmacological processes. In addition, perturbation of SLC transporter function underlies numerous human diseases, which renders SLC transporters attractive drug targets. Common genetic polymorphisms in SLC genes have been associated with inter-individual differences in drug efficacy and toxicity. However, despite their tremendous clinical relevance, epidemiological data of these variants are mostly derived from heterogeneous cohorts of small sample size and the genetic SLC landscape beyond these common variants has not been comprehensively assessed. In this study, we analyzed Next-Generation Sequencing data from 141,456 individuals from seven major human populations to evaluate genetic variability, its functional consequences, and ethnogeographic patterns across the entire SLC superfamily of transporters. Importantly, of the 204,287 exonic single-nucleotide variants (SNVs) which we identified, 99.8% were present in less than 1% of analyzed alleles. Comprehensive computational analyses using 13 partially orthogonal algorithms that predict the functional impact of genetic variations based on sequence information, evolutionary conservation, structural considerations, and functional genomics data revealed that each individual genome harbors 29.7 variants with putative functional effects, of which rare variants account for 18%. Inter-ethnic variability was found to be extensive, and 83% of deleterious SLC variants were only identified in a single population. Interestingly, population-specific carrier frequencies of loss-of-function variants in SLC genes associated with recessive Mendelian disease recapitulated the ethnogeographic variation of the corresponding disorders, including cystinuria in Jewish individuals, type II citrullinemia in East Asians, and lysinuric protein intolerance in Finns, thus providing a powerful resource for clinical geneticists to inform about population-specific prevalence and allelic composition of Mendelian SLC diseases. In summary, we present the most comprehensive data set of SLC variability published to date, which can provide insights into inter-individual differences in SLC transporter function and guide the optimization of population-specific genotyping strategies in the bourgeoning fields of personalized medicine and precision public health.

Approaches to triage optimization in HPV primary screening: Extended genotyping and p16/Ki‐67 dual‐stained cytology—Retrospective insights from ATHENA

The objective of our study was to assess the performance of different triage strategies for high‐risk human papillomavirus (hrHPV)‐positive results utilizing either extended genotyping or a p16/Ki‐67 dual‐stained cytology (DS) approach, with or without partial genotyping. A subset of women with hrHPV infections participating in the Addressing the Need for Advanced HPV Diagnostics (ATHENA) study were analyzed to determine the number of cervical intraepithelial neoplasia grade 3 or worse (≥CIN3) cases detected, and the absolute risk for ≥CIN3 of each genotype. A clinical utility table was constructed to compare the impact of different triage strategies. In all, 2,339 women with single‐genotype hrHPV infections were identified. Among these were 171 ≥CIN3 cases. The U.S. Food and Drug Administration (FDA)‐approved algorithm (HPV16/18 positive, or 12‐other hrHPV positive and Pap positive, i.e., ≥ atypical squamous cells of undetermined significance) for primary HPV screening detected 132/171 (77.2%) ≥CIN3 cases and required 964 colposcopies (colposcopies per ≥CIN3 ratio: 7.3). An approach that uses DS instead of cytology in the FDA‐approved algorithm detected 147/171 (86.0%) ≥CIN3 cases, requiring 1,012 colposcopies (ratio: 6.9). Utilizing DS for triage of all hrHPV‐positive women identified 126/171 (73.7%) ≥CIN3 cases, requiring 640 colposcopies (ratio: 5.1). A strategy that detected HPV16/18/31/33/35+ captured 130/171 (76.0%) ≥CIN3 cases, requiring 1,025 colposcopies (ratio: 7.9). Inclusion of additional genotypes resulted in greater disease detection at the expense of higher colposcopy ratios. Substituting cytology with a DS triage approach improved disease detection and the colposcopy detection rate. Further reduction of colposcopy rates can be achieved by using DS without partial genotyping. Extended genotyping strategies can identify a comparable number of cases but requires an increased number of colposcopies.

Optimizing PCR for Mouse Genotyping: Recommendations for Reliable, Rapid, Cost Effective, Robust and Adaptable to High-Throughput Genotyping Protocol for Any Type of Mutation.

Genotyping consists of searching for a DNA sequence variation localized at a well-defined locus in the genome. It is an essential step in animal research because it allows the identification of animals that will be bred to generate and maintain a colony, euthanized to control the available space in the animal facility, or used in experiment protocols. Here we describe polymerase chain reaction (PCR) genotyping protocols for fast, sensitive, easy, and cost-effective characterization of mouse genotype. We discuss optimization of parameters to improve the reliability of each assay and propose recommendations for enhancing reproducibility and reducing the occurrence of inconclusive genotyping. All steps required for efficient genotyping are presented: tissue collection; sample verification and direct DNA lysis; establishment of a robust genotyping strategy with reliable, rapid, and cost-effective assays; and finally, transition to high-throughput automatized PCR, including mix miniaturization and automation. © 2019 The Authors. Basic Protocol 1: Tissue sampling methods and procedure Basic Protocol 2: Sample verification and DNA lysis Basic Protocol 3: Design of a genotyping strategy Basic Protocol 4: Moving to high-throughput genotyping.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study

BackgroundFermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. Among them, high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes.ResultsIn this study, three QTLs linked to stuck fermentation in winemaking conditions were identified by using a selective genotyping strategy carried out on a backcrossed population. The precision of mapping allows the identification of two causative genes VHS1 and OYE2 characterized by stop-codon insertion. The phenotypic effect of these allelic variations was validated by Reciprocal Hemyzygous Assay in high gravity fermentations (> 240 g/L of sugar) carried out at high temperatures (> 28 °C). Phenotypes impacted were mostly related to the late stage of alcoholic fermentation during the stationary growth phase of yeast.ConclusionsOur findings illustrate the complex genetic determinism of stuck fermentation and open new avenues for better understanding yeast resistance mechanisms involved in high gravity fermentations.

Genetic Diversity of Brucella melitensis in Kazakhstan in Relation to World-Wide Diversity.

We describe the genetic diversity of 1327 Brucella strains from human patients in Kazakhstan using multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA). All strains were assigned to the Brucella melitensis East Mediterranean group and clustered into 16 MLVA11 genotypes, nine of which are reported for the first time. MLVA11 genotype 116 predominates (86.8%) and is present all over Kazakhstan indicating existence and temporary preservation of a “founder effect” among B. melitensis strains circulating in Central Eurasia. The diversity pattern observed in humans is highly similar to the pattern previously reported in animals. The diversity observed by MLVA suggested that the epidemiological status of brucellosis in Kazakhstan is the result of the introduction of a few lineages, which have subsequently diversified at the most unstable tandem repeat loci. This investigation will allow to select the most relevant strains for testing these hypotheses via whole genome sequencing and to subsequently adjust the genotyping scheme to the Kazakhstan epidemiological situation.

Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice

BackgroundIntegrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results.ResultsEvaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations.ConclusionThis study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.

In Vivo Single-Cell Genotyping of Mouse Cortical Neurons Transfected with CRISPR/Cas9

CRISPR/Cas-based technologies have revolutionized genetic approaches to addressing a wide range of neurobiological questions. The ability of CRISPR/Cas to introduce mutations into target genes allows us to perform invivo loss-of-function experiments without generating genetically engineered mice. However, the lack of a reliable method to determine genotypes of individual CRISPR/Cas-transfected cells has made it impossible to unambiguously identify the genetic cause of their phenotypes invivo. Here, we report a strategy for single-cell genotyping in CRISPR/Cas-transfected neurons that were phenotypically characterized invivo. We show that re-sectioning of cortical slices and subsequent lasermicrodissection allow us to isolate individual CRISPR/Cas-transfected neurons. Sequencing of PCR products containing a CRISPR/Cas-targeted genomic region in single reference neurons provided genotypes that completely correspond with those deduced from their target protein expression and phenotypes. Thus, our study establishes a powerful strategy to determine the causality between genotypes and phenotypes in CRISPR/Cas-transfected neurons.

Variation in the μ-Opioid Receptor Gene (OPRM1) Does Not Moderate Social-Rejection Sensitivity in Humans

Given previous findings from animal studies and small-scale studies in humans, variation in the μ-opioid receptor gene (OPRM1) has been proposed as a strong biological candidate for moderating sensitivity to social rejection. Using a substantially larger sample (N = 490) than previous studies, a prospective genotyping strategy, and preregistered analysis plans, we tested the hypotheses that OPRM1 variation measured by the functional A118G polymorphism (rs1799971) moderates (a) dispositional sensitivity to rejection and feelings of distress following social exclusion and (b) decision making involving social cognition. In three experimental tasks commonly used to assess altruism, reciprocity, and trust in humans, we found no evidence in favor of the hypotheses; nine main tests were preregistered, and all of them yielded small and statistically insignificant estimates. In secondary analyses, we used Bayesian inference and estimation to quantify support for our findings. Taken together, our results strongly suggest that the link between OPRM1 A118G variation and social-rejection sensitivity is weaker than previously thought.

P015 CFTR RealTime Panel using pre-plated LightSNiP assays is a good strategy for CFTR genotyping

P015 CFTR RealTime Panel using pre-plated LightSNiP assays is a good strategy for CFTR genotyping

Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.

Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.