Molecular Biology at the bedside: the impact of Genomics on the practice of medicine

Imagine being a newborn baby, discharged home after delivery, with a most unusual gift, a compact disc (CD) carrying all data on "My Genome". The parents would be most anxious to play it on their home PC. Soon, they could discover whether their child has been spared those major single gene disorders which uncle John had before he died young. The doctors had told them they could be selected out when they had opted for pre-gestational diagnosis and selective fertilisation.peer-reviewe

LifeTime and improving European healthcare through cell-based interceptive medicine

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade

Identification of ADHD risk genes in extended pedigrees by combining linkage analysis and whole-exome sequencing

Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder with a complex genetic background, hampering identification of underlying genetic risk factors. We hypothesized that combining linkage analysis and whole-exome sequencing (WES) in multi-generation pedigrees with multiple affected individuals can point toward novel ADHD genes. Three families with multiple ADHD-affected members (Ntotal = 70) and apparent dominant inheritance pattern were included in this study. Genotyping was performed in 37 family members, and WES was additionally carried out in 10 of those. Linkage analysis was performed using multi-point analysis in Superlink Online SNP 1.1. From prioritized linkage regions with a LOD score ≥ 2, a total of 24 genes harboring rare variants were selected. Those genes were taken forward and were jointly analyzed in gene-set analyses of exome-chip data using the MAGMA software in an independent sample of patients with persistent ADHD and healthy controls (N = 9365). The gene-set including all 24 genes together, and particularly the gene-set from one of the three families (12 genes), were significantly associated with persistent ADHD in this sample. Among the latter, gene-wide analysis for the AAED1 gene reached significance. A rare variant (rs151326868) within AAED1 segregated with ADHD in one of the families. The analytic strategy followed here is an effective approach for identifying novel ADHD risk genes. Additionally, this study suggests that both rare and more frequent variants in multiple genes act together in contributing to ADHD risk, even in individual multi-case families

Unraveling the Genetic Mysteries of the Norwegian Fjord-horse: Identifying Harmful Haplotypes for Improved Breeding Strategies

Fertiliteten til avlsdyrene er særdeles kritisk i små populasjoner med høy innavl. Fjordhest- populasjonen i Norge består av få stamfedre, og er blitt registrert til å ha en lavere føllings-rate enn flere andre hesteraser. Denne analysen er basert på høy-tetthets SNP genotyper fra ca. 330 Fjordhester. For å identifisere mulige resessive dødelige alleler undersøkes genomet for homozygote avvik i haplotyper. Signifikante avvik i haplotyper med én eller mindre observerte homozygoter ble karakterisert som kandidat-loci. Deretter, vil kandidat-loci analyseres i forhold til funksjonell kunnskap om genomet til hest, menneske og mus. Kandidatgenene som dette studiet kommer frem til er DEAF5L, DEFA22, KIA1109, og DPF2.The fertility in breeding-animals is especially critical in small populations in which there is a high degree of inbreeding. The Norwegian Fjord-horse population consists of few founder animals and is observed to underperform in foaling rate compared to several other horse breeds. The project is based on HD SNP genotypes from approximately 330 Fjord-horses. In order to identify potential recessive lethal alleles, the haplotype homozygote deficiencies were identified. Significant haplotypes with one or fewer homozygotes observed were characterized as the candidate loci. Further, the candidate loci were aligned with functional knowledge of equine, human, and mouse genomes. Candidate genes identified by this study were DEFA5L, DEFA22, KIA1109, and DPF2

Phenotypic and Genetic Factors Associated with Absence of Cardiomyopathy Symptoms in PLN:c.40_42delAGA Carriers

The c.40_42delAGA variant in the phospholamban gene (PLN) has been associated with dilated and arrhythmogenic cardiomyopathy, with up to 70% of carriers experiencing a major cardiac event by age 70. However, there are carriers who remain asymptomatic at older ages. To understand the mechanisms behind this incomplete penetrance, we evaluated potential phenotypic and genetic modifiers in 74 PLN:c.40_42delAGA carriers identified in 36,339 participants of the Lifelines population cohort. Asymptomatic carriers (N = 48) showed shorter QRS duration (− 5.73 ms, q value = 0.001) compared to asymptomatic non-carriers, an effect we could replicate in two different independent cohorts. Furthermore, symptomatic carriers showed a higher correlation (r Pearson = 0.17) between polygenic predisposition to higher QRS (PGSQRS) and QRS (p value = 1.98 × 10–8), suggesting that the effect of the genetic variation on cardiac rhythm might be increased in symptomatic carriers. Our results allow for improved clinical interpretation for asymptomatic carriers, while our approach could guide future studies on genetic diseases with incomplete penetrance. Graphical abstract: [Figure not available: see fulltext.].</p

Phenotypic and Genetic Factors Associated with Absence of Cardiomyopathy Symptoms in PLN:c.40_42delAGA Carriers

The c.40_42delAGA variant in the phospholamban gene (PLN) has been associated with dilated and arrhythmogenic cardiomyopathy, with up to 70% of carriers experiencing a major cardiac event by age 70. However, there are carriers who remain asymptomatic at older ages. To understand the mechanisms behind this incomplete penetrance, we evaluated potential phenotypic and genetic modifiers in 74 PLN:c.40_42delAGA carriers identified in 36,339 participants of the Lifelines population cohort. Asymptomatic carriers (N = 48) showed shorter QRS duration (− 5.73 ms, q value = 0.001) compared to asymptomatic non-carriers, an effect we could replicate in two different independent cohorts. Furthermore, symptomatic carriers showed a higher correlation (rPearson = 0.17) between polygenic predisposition to higher QRS (PGSQRS) and QRS (p value = 1.98 × 10–8), suggesting that the effect of the genetic variation on cardiac rhythm might be increased in symptomatic carriers. Our results allow for improved clinical interpretation for asymptomatic carriers, while our approach could guide future studies on genetic diseases with incomplete penetrance.</p

Genetic characterization of Mandevilla spp. experimental lines by gSSR genotyping and cpDNA barcoding.

Mandevilla is a genus comprehending several ornamental plant species with a brilliant future overall in view of its high business acknowledgment and added esteem. Its nomenclature also includes Dipladenia, while its common name is “Brazilian jasmine” and is a decorative plant that was brought into the European market around 150 years ago. Until 1955, its development was limited to experienced English landscapers, and it was then spread all through Europe by Danish horticulturists. At present, this plant can be tracked down covering overhangs, lattices, arbores, and scenes, adding a tropical style to any open-air space. Mandevilla is particularly valued for its remarkable protection from wind, dry season, and pungent air, making it an ideal flower for summer in the Mediterranean region. However, like most ornamental crops, there are very few molecular tools that could be used for the purpose of cultivar innovation and breeding. In this research work, we report the development and analysis of 23 Simple Sequence Repeat (SSR) markers in Mandevilla. The microsatellites used in the work were developed and isolated from a newly arranged draft genome of the sample named “2001”. The developed markers were thus evaluated on a Mandevilla core collection, consisting of 55 samples of breeding and pre-commercial value, to determine the discrimination capability of the molecular markers panel, to characterize the core collection genotypes, and for evaluating the genetic similarity and genetic structure of the core collection in the exam. Moreover, a DNA barcoding approach was also performed to investigate the species ancestry, since most of the genotypes available are probably interspecific hybrids, characterized by complex genealogies. The analysis parameters were estimated after the amplification of the samples, a very garbled scenario, due to interspecific crosses. Based on the genetic similarity matrix, 7 comparisons were found to have 100% genetic similarity and the least genetic similarity was identified to be 50.2%. Genetic structure analysis revealed that the most probable number of ancestors constituting the core collection was equal to 26. The observation of admixed patterns was interpreted as a consequence of interspecific crosses that took place to obtain required morphological characters throughout the centuries. DNA barcoding and haplotyping analysis based on the rbcL and ITS1 genes divided samples into two clusters indicating their maternal inheritance patterns. Overall molecular data highlighted that the core collection of Mandevilla analyzed in this study has a very complex genetic structure and is characterized by high genetic diversity. Thus, the molecular markers understudy could find utility in breeding programs aimed at the selection of valuable experimental lines well adapted to the agronomic and environmental conditions, and in genetic traceability studies of the Mandevilla spp.Mandevilla is a genus comprehending several ornamental plant species with a brilliant future overall in view of its high business acknowledgment and added esteem. Its nomenclature also includes Dipladenia, while its common name is “Brazilian jasmine” and is a decorative plant that was brought into the European market around 150 years ago. Until 1955, its development was limited to experienced English landscapers, and it was then spread all through Europe by Danish horticulturists. At present, this plant can be tracked down covering overhangs, lattices, arbores, and scenes, adding a tropical style to any open-air space. Mandevilla is particularly valued for its remarkable protection from wind, dry season, and pungent air, making it an ideal flower for summer in the Mediterranean region. However, like most of the ornamental crops, there are very few molecular tools that could be used for the purpose of cultivar innovation and breeding. In this research work, we report the development and analysis of 23 Simple Sequence Repeat (SSR) markers in Mandevilla. The microsatellites used in the work were developed and isolated from a newly arranged draft genome of the sample named “2001”. The developed markers were thus evaluated on a Mandevilla core collection, consisting of 55 samples of breeding and pre-commercial value, to determine the discrimination capability of the molecular markers panel, to characterize the core collection genotypes, and for evaluating the genetic similarity and genetic structure of the core collection in exam. Moreover, a DNA barcoding approach was also performed to investigate the species ancestry, since most of the genotypes available are probably interspecific hybrids, characterized by complex genealogies. The analysis parameters estimated after the amplification of the samples, a very garbled scenario, due to interspecific crosses. Based on the genetic similarity matrix, 7 comparisons were found to have 100% genetic similarity and the least genetic similarity was identified to be 50.2%. Genetic structure analysis revealed that the most probable number of ancestors constituting the core collection was equal to 26. The observation of admixed patterns was interpreted as a consequence of interspecific crosses that took place to obtain required morphological characters throughout the centuries. DNA barcoding and haplotyping analysis based on the rbcL and ITS1 genes divided samples into two clusters indicating their maternal inheritance patterns. Overall molecular data highlighted that the core collection of Mandevilla analyzed in this study has a very complex genetic structure and is characterized by high genetic diversity. Thus, the molecular markers under study could find utility in breeding programs aimed at the selection of valuable experimental lines well adapted to the agronomic and environmental conditions, and in genetic traceability studies of the Mandevilla spp

Genetic Determinism of Xanthomonas arboricola pv. pruni (Xap) Resistance, Fruit Quality, and Phenological Traits in Peach and Incorporation of Marker-Assisted Selection (MAS) in the University of Arkansas Peach and Nectarine Breeding Program

For over two decades the incorporation of marker-assisted selection (MAS) has been discussed as an innovative approach to increase peach breeding efficiency. Although hundreds of quantitative trait loci (QTLs) have been identified, only a few have been converted into usable MAS tools. This highlights a disconnect between genomic discoveries and practical application in breeding programs, which has delayed use of MAS. In this dissertation, three sequential steps were performed with the objective to bridge this gap and develop breeding-relevant DNA tests for MAS of fruit bacterial spot resistance (Xap1 and Xap6), fruit quality [blush (Rf), acidity (D), and acidity and soluble solid content (G7Flav)], and phenological traits [maturity date (G4mat), fruit type (G), and flesh color (Y)] across four RosBREED peach breeding programs. First, previously identified QTLs were further investigated and 32 SNPs were grouped into haplotypes and validated for association with breeding-relevant trait differences across RosBREED germplasm. The SNPs were divided into two mini-arrays and advanced breeding material from all programs were outsourced for design and testing. The validated SNP loci were used in marker-assisted parent selection (MAPS) in 2013-2015 at the University of Arkansas (UA) program to combine horizontal Xap resistance with high fruit quality spanning the season. Secondly, four of the SNP-based tests (Xap1, Xap6, G, and Y loci) were converted into sequence length polymorphism-based (SLP-based) tests (Ppe-XapF1-SSR, Ppe-XapF6-SSR, indelG, and PpCCD4b-SSR) and screened on the UA RosBREED germplasm and 22 additional F1 populations. Results were compared across both DNA tests to identify the most efficient genotyping approach for each trait. In 2015, two of the SLP-based DNA tests, the indelG (pubescent vs. glabrous) and PpCCD4b-SSR (white vs. yellow flesh) were advanced to test in marker-assisted seedling selection (MASS). In the final step, QTL analysis was conducted for Xap fruit, Xap leaf, and Xap leaf-assay resistance along with seven fruit quality and phenological traits using the Pedigree-Based Analysis (PBA) approach and the UA RosBREED pedigree. Overall 20 QTLs were identified, 10 for Xap resistance and 10 for quality and phenological traits. These 20 QTLs are optimal targets for future DNA test development, validation, and use in MAS