Mosaic Conditions Research Articles

Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless

BackgroundSignificant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes.MethodsUnsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery.ResultsIn total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype–phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP.ConclusionAHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.

Exploring New Drug Repurposing Opportunities for MEK Inhibitors in RASopathies: A Comprehensive Review of Safety, Efficacy, and Future Perspectives of Trametinib and Selumetinib.

The RASopathies are a group of syndromes caused by genetic variants that affect the RAS-MAPK signaling pathway, which is essential for cell response to diverse stimuli. These variants functionally converge towards the overactivation of the pathway, leading to various constitutional and mosaic conditions. These syndromes show overlapping though distinct clinical presentations and share congenital heart defects, hypertrophic cardiomyopathy (HCM), and lymphatic dysplasia as major clinical features, with highly variable prevalence and severity. Available treatments have mainly been directed to target the symptoms. However, repurposing MEK inhibitors (MEKis), which were originally developed for cancer treatment, to target evolutive aspects occurring in these disorders is a promising option. Animal models have shown encouraging results in treating various RASopathy manifestations, including HCM and lymphatic abnormalities. Clinical reports have also provided first evidence supporting the effectiveness of MEKi, especially trametinib, in treating life-threatening conditions associated with these disorders. Nevertheless, despite notable improvements, there are adverse events that occur, necessitating careful monitoring. Moreover, there is evidence indicating that multiple pathways can contribute to these disorders, indicating a current need to more accurate understand of the underlying mechanism of the disease to apply an effective targeted therapy. In conclusion, while MEKi holds promise in managing life-threatening complications of RASopathies, dedicated clinical trials are required to establish standardized treatment protocols tailored to take into account the individual needs of each patient and favor a personalized treatment.

Correspondence Concerning PTPN11 Mosaicism Causes a Spectrum of Pigmentary and Vascular Neurocutaneous Disorders and Predisposes to Melanoma

I read with great interest the article by Polubuthu et al. reporting on the detection of PTPN11 mutations in several mosaic conditions, i.e. phacomatosis spilorosea, nevus spilus, nevus roseus and speckled lentiginous nevus syndrome (Polubuthu et al., [in press]). One of the paper’s conclusions is that mosaic PTPN11 mutations in nevus spilus predispose to cutaneous melanoma. I wish to challenge such conclusion based on the following points.

Confirmatory test versus screening test analyses for fetal mosaic variations; a large scale study

ABSTRACT Background Mosaic genetic anomaly is a problematic and interpretative issue in prenatal diagnosis. Conventional karyotyping, as a confirmatory test traditionally used for detecting mosaic and nonmosiac prenatal disorders. Recently Quantitative Fluorescence PCR (QF-PCR) is used for prenatal testing. We retrospectively assessed the frequency of both mosaic and nonmosaic conditions in a large-scale study and compared the clinical value of confirmatory cytogenetic analysis with QF-PCR and other screening tests. Result Of 6033 cases identified as abnormal conditions by sonography or protein marker screening tests, only 180 nonmosaic and 8 mosaic cases confirmed to be abnormal by confirmatory karyotyping test results. The cytogenetic analysis was correlated with other QF-PCR confirmatory test results for nonmosiac conditions but it was not comparable for mosaic cases. Conclusion The cytogenetic analyses were shown to have the greatest clinical value in revealing the various mosaic conditions. The QF-PCR test is shown to be a reliable confirmatory test for nonmosaic diseases but not for mosaicism, and the screening protein marker test can weakly indicate the presence of abnormal cell lines. Moreover, older mothers (>30 years) are at greater risk for developing mosaic ova.

Somatic mosaics in hereditary tumor predisposition syndromes

Historically, it is estimated that 5–10% of cancer patients carry a causative genetic variant for a tumor predisposition syndrome. These conditions have high clinical relevance as they are actionable regarding risk-specific surveillance, predictive genetic testing, reproductive options, and – in some cases – risk reducing surgery or targeted therapy. Every individual is born with on average 0.5–1 exonic mosaic variants prevalent in single or multiple tissues. Depending on the tissues affected, mosaic conditions can abrogate the clinical phenotype of a tumor predisposition syndrome and can even go unrecognized, because it can be impossible or difficult to detect them with routine genetic testing in blood/leucocytes. On the other hand, it is estimated that at least 4% of presumed de novo variants are the result of low-level mosaicism (variant allele frequency <10%) in a parent, while around 7% are true mosaic variants with a higher variant allele frequency, which can sometimes be confused for heterozygous variants. Clonal hematopoiesis however can simulate a mosaic tumor predisposition in genetic diagnostics and has to be taken into account, especially for TP53 variants.Depending on the technique, variant allele frequencies of 2–3% can be detected for single nucleotide variants by next generation sequencing, copy number variants with variant allele frequencies of 5–30% can be detected by array-based technologies or MLPA.Mosaic tumor predisposition syndromes are more common than previously thought and may often remain undiagnosed. The clinical suspicion and diagnostic procedure for several cases with mosaic tumor predisposition syndromes are presented.

Association Between Dieting Failure and Unconscious Hedonic Responses to Food.

Dieting is a popular but difficult strategy for reducing weight. Previous studies have revealed several psychological characteristics associated with dieting failure. Here, the hypothesis that dieting failure is associated with unconscious hedonic responses to food was tested with a subliminal affective priming task. Food image primes or their scrambled mosaic primes were subliminally presented. Participants scored their liking of the subsequent target ideographs. The participants’ subjective dieting success was additionally assessed using questionnaires. Differences in liking scores of target ideographs between the food and mosaic conditions, as well as liking scores of target ideographs under the food condition by partialing-out other effects, were negatively associated with dieting success scores. These results suggest that dieting failure is associated with the strength of unconscious hedonic responses to food and that environmental controls to reduce food cues may be needed for dieting success.

Bird Diversity as a Support Decision Tool for Sustainable Management in Temperate Forested Floodplain Landscapes

Sustainably managed forests provide multiple ecosystem services in cultural landscapes, including maintaining biodiversity. Better understanding of the benefits regarding the biodiversity of different silvicultural practices is important for sustainable landscape management. Conservation targets in forested landscapes should be determined by land managers and policy-makers, based on serious ecological research. This study deals with response of bird diversity to three different habitat types of temperate hardwood floodplain forests, which reflect specific forms of forest management. Research was based on long-term field bird census in the years 1998 to 2002 applying the point count method. Data was analysed using regression analysis with dummy variables. The results of the study indicate that hardwood floodplain forest heterogeneity, supported by different types of forest management (old-growth forest protection, group-selection harvesting and forest edge protection), provides large-scale habitat mosaic conditions suitable for many breeding bird species with different ecological niches. This result suggests that comparison of bird diversity response to different forest management types can be used as a decision support tool for sustainable landscape management strategy and local management practices in forested cultural lowland landscapes. Improvements in both regional and local ecological knowledge are generally needed in order to control floodplain land use decisions, which are typically made on the scale of landscape management.

Fossil snakes (Squamata, Serpentes) from the tar pits of Venezuela: taxonomic, palaeoenvironmental, and palaeobiogeographical implications for the North of South America during the Cenozoic/Quaternary boundary.

BackgroundTar seep deposits in South America historically are well-known for their rich record of fossil mammals, contrasting with only a few formal reports of reptile remains. Here we report a new snake fauna recovered from two tar pits from Venezuela. The fossil remains come from two localities: (a) El Breal de Orocual, which comprises an inactive tar seep estimated to be Plio/Pleistocene in age; and (b) Mene de Inciarte, an active surface asphalt deposit with an absolute age dating to the late Pleistocene.MethodsThe taxonomic identity of all specimens was assessed via consultation of the relevant literature and comparison with extant specimens. The taxonomic assignments are supported by detailed anatomical description.ResultsThe Mene de Inciarte snake fauna comprises vertebral remains identified as the genus Epicrates sp. (Boidae), indeterminate viperids, and several isolated vertebrae attributable to “Colubridae” (Colubroidea, sensu Zaher et al., 2009). Amongst the vertebral assemblage at El Breal de Orocual, one specimen is assigned to the genus Corallus sp. (Boidae), another to cf. Micrurus (Elapidae), and several others to “Colubrids” (Colubroides, sensu Zaher et al., 2009) and the Viperidae family.ConclusionsThese new records provide valuable insight into the diversity of snakes in the north of South America during the Neogene/Quaternary boundary. The snake fauna of El Breal de Orocual and Mene de Inciarte demonstrates the presence of Boidae, Viperidae, “colubrids”, and the oldest South American record of Elapidae. The presence of Corallus, Epicrates, and viperids corroborates the mosaic palaeoenvironmental conditions of El Breal de Orocual. The presence of Colubroides within both deposits sheds light on the palaeobiogeographical pattern of caenophidians snake colonization of South America and is consistent with the hypothesis of two episodes of dispersion of Colubroides to the continent.

Mosaicism for GNAS methylation defects associated with pseudohypoparathyroidism type 1B arose in early post-zygotic phases

BackgroundPseudohypoparathyroidism type 1B (PHP1B; MIM#603233) is a rare imprinting disorder (ID), associated with the GNAS locus, characterized by parathyroid hormone (PTH) resistance in the absence of other endocrine or physical abnormalities. Sporadic PHP1B cases, with no known underlying primary genetic lesions, could represent true stochastic errors in early embryonic maintenance of methylation. Previous data confirmed the existence of different degrees of methylation defects associated with PHP1B and suggested the presence of mosaicism, a phenomenon already described in the context of other IDs.ResultsWith respect to mosaic conditions, the study of multiple tissues is a necessary approach; thus, we investigated somatic cell lines (peripheral blood and buccal epithelium and cells from the urine sediment) descending from different germ layers from 19 PHP patients (11 spor-PHP1B, 4 GNAS mutated PHP1A, and 4 PHP with no GNAS (epi)genetic defects) and 5 healthy controls. We identified 11 patients with epigenetic defects, further subdivided in groups with complete or partial methylation defects. The recurrence of specific patterns of partial methylation defects limited to specific CpGs was confirmed by checking methylation profiles of spor-PHP1B patients diagnosed in our lab (n = 56). Underlying primary genetic defects, such as uniparental disomy or deletion, potentially causative for the detected partial methylation were excluded in all samples.ConclusionsOur data showed no differences of methylation levels between organs and tissues from the same patient, so we concluded that the epimutation occurred in early post-zygotic phases and that the partial defects were mosaics. The number of patients with no detectable (epi)genetic GNAS defects was too small to exclude epimutations occurring in later post-zygotic phases, affecting only selected tissues different from blood, thus leading to underdiagnosis during routine molecular diagnosis. Finally, we found no correlation between methylation ratios, representing the proportion of epimutated cells, and the clinical presentation, further confirming the hypothesis of a threshold effect of the GNAS loss of imprinting leading to an “all-or-none” phenotype.

Моніторинг лісів Розточчя як системна складова поліфункційного сталого лісового господарства

У рамках програми комплексного моніторингу лісів, що грунтується на основі використання сучасних дистанційних і наземних методів збору та оброблення інформації, описано просторову структуру лісових масивів Українського Розточчя. Для цього використано супутникові знімки Landsat 5 TM, Landsat 7 ETM+, QuikBird Transnavikom Ltd. та Cnes/Spot. На їх основі побудовано карти розподілу лісових масивів, обчислено їх достовірність та зроблено висновки щодо структури. Розраховано растрову сітку розміщення пробних площ на досліджуваній території. Опрацьовано та доповнено методику збору й оброблення отриманої інформації.

Homeostatic modulation on unconscious hedonic responses to food

Hedonic/affective responses to food play a critical role in eating behavior. Previous behavioral studies have shown that hedonic responses to food are elicited consciously and unconsciously. Although the studies also showed that hunger and satiation have a modulatory effect on conscious hedonic responses to food, the effect of these homeostatic states on unconscious hedonic responses to food remains unknown. We investigated unconscious hedonic responses to food in hungry and satiated participants using the subliminal affective priming paradigm. Food images or corresponding mosaic images were presented in the left or right peripheral visual field during 33 ms. Then photographs of target faces with emotionally neutral expressions were presented, and the participants evaluated their preference for the faces. Additionally, daily eating behaviors were assessed using questionnaires. Preference for the target faces was increased by food images relative to the mosaics in the hungry, but not the satiated, state. The difference in preference ratings between the food and mosaic conditions was positively correlated with the tendency for external eating in the hungry, but not the satiated, group. Our findings suggest that homeostatic states modulate unconscious hedonic responses to food and that this phenomenon is related to daily eating behaviors.

Mosaic Disorders of the PI3K/PTEN/AKT/TSC/mTORC1 Signaling Pathway.

Somatic mutations in genes of the PI3K/PTEN/AKT/TSC/mTORC1 signaling pathway cause segmental overgrowth, hamartomas, and malignant tumors. Mosaicism for activating mutations in AKT1 or PIK3CA cause Proteus syndrome and PIK3CA-Related Overgrowth Spectrum, respectively. Postzygotic mutations in PTEN or TSC1/TSC2 cause mosaic forms of PTEN hamartoma tumor syndrome or tuberous sclerosis complex, respectively. Distinct features observed in these mosaic conditions in part reflect differences in embryological timing or tissue type harboring the mutant cells. Deep sequencing of affected tissue is useful for diagnosis. Drugs targeting mTORC1 or other points along this signaling pathway are in clinical trials to treat these disorders.

Whole-Genome Sequencing and iPLEX MassARRAY Genotyping Map an EMS-Induced Mutation Affecting Cell Competition in Drosophila melanogaster.

Cell competition, the conditional loss of viable genotypes only when surrounded by other cells, is a phenomenon observed in certain genetic mosaic conditions. We conducted a chemical mutagenesis and screen to recover new mutations that affect cell competition between wild-type and RpS3 heterozygous cells. Mutations were identified by whole-genome sequencing, making use of software tools that greatly facilitate the distinction between newly induced mutations and other sources of apparent sequence polymorphism, thereby reducing false-positive and false-negative identification rates. In addition, we utilized iPLEX MassARRAY for genotyping recombinant chromosomes. These approaches permitted the mapping of a new mutation affecting cell competition when only a single allele existed, with a phenotype assessed only in genetic mosaics, without the benefit of complementation with existing mutations, deletions, or duplications. These techniques expand the utility of chemical mutagenesis and whole-genome sequencing for mutant identification. We discuss mutations in the Atm and Xrp1 genes identified in this screen.

Melanocytic naevi clustered on normal background skin.

Several types of maculopapular melanocytic naevi can occur in a multiple form, and be arranged in a nonrandom fashion on the skin. The most frequently reported segmentally grouped naevi are lentigines. Two types of segmentally arranged lentigines probably exist. The first is associated with neurofibromatosis (NF)1 or NF1 signs, features scattered light-brown lesions and can be considered a type of mosaic NF1. By contrast, non-NF1 associated lesions are characterized by densely packed, dark lesions, and can be defined as 'non-NF1 checkerboard-arranged lentigines'. Blue naevi, Spitz naevi and common acquired melanocytic naevi can occur, clustered in an agminated (or cannonball) shape. However, if large enough, they always follow a checkerboard pattern. Hence, such mosaic conditions should be termed 'checkerboard-arranged blue naevi', 'checkerboard-arranged Spitz naevi' and 'checkerboard-arranged common acquired melanocytic naevi'. Segmentally arranged dysplastic melanocytic naevi probably represent a mosaic form of dysplastic naevus syndrome. Dysplastic melanocytic naevi confined to a cutaneous segment could be defined as 'isolated segmental dysplastic naevus syndrome', while segmentally arranged dysplastic melanocytic naevi co-occurring with widespread, nonsegmental dysplastic melanocytic naevi might configure a 'superimposed segmental dysplastic naevus syndrome'. Small congenital melanocytic naevi are always grouped along Blaschko lines. The only other instances following Blaschko lines are the so-called 'linear lentiginous naevus' and a unique case of multiple deep penetrating naevi.

45,X/47,XXX Mosaicism and Short Stature.

We describe the case of a ten-year-old girl with short stature and 45,X/47,XXX genotype. She also suffered from vesicoureteric reflux and kidney dysfunction prior to having surgery on her ureters. Otherwise, she does not have any of the characteristics of Turner nor Triple X syndrome. It has been shown that this mosaic condition as well as other varieties creates a milder phenotype than typical Turner syndrome, which is what we mostly see in our patient. However, this patient is a special case, because she is exceptionally short. Overall, one cannot predict the resultant phenotype in these mosaic conditions. This creates difficulty in counseling parents whose children or fetuses have these karyotypes.

New BAC probe set to narrow down chromosomal breakpoints in small and large derivative chromosomes, especially suited for mosaic conditions.

Fluorescence in situ hybridization (FISH) and/or array-comparative genomic hybridization (aCGH) performed after initial banding cytogenetics is still the gold standard for detection of chromosomal rearrangements. Although aCGH provides a higher resolution, FISH has two main advantages over the array-based approaches: (1) it can be applied to characterize balanced as well as unbalanced rearrangements, whereas aCGH is restricted to unbalanced ones, and (2) chromosomal aberrations present in low level or complex mosaics can be characterized by FISH without any problems, while aCGH requires presence of over 50 % of aberrant cells in the sample for detection. Recently, a new FISH-based probe set was presented: the so-called pericentric-ladder-FISH (PCL-FISH) that enables characterization of chromosomal breakpoints especially in mosaic small supernumerary marker chromosomes (sSMC). It can also be applied on large inborn or acquired derivative chromosomes. The main feature of this set is that the probes are applied in a chromosome-specific manner and they align along the chromosome in average intervals of ten megabasepairs. Hence PCL-FISH provides denser coverage and a more precise anchorage on the human DNA-sequence than most other FISH-banding approaches.

Oral Pigmentation in McCune-Albright Syndrome

The differential diagnosis for oral lentigines includes several syndromes with important associated systemic findings. McCune-Albright syndrome (MAS), a mosaic condition associated with café au lait pigmentation, is not typically considered a mucosal lentiginosis syndrome. The clinical phenotype of MAS is variable because of mosaicism, but oral pigmentation developing in mid-childhood to early adulthood should be recognized as a clinical feature of MAS. We present 4 patients with MAS who developed oral mucosal pigmentation during childhood or early adulthood. All patients had other characteristic findings of MAS including hyperfunctioning endocrinopathies, polyostotic fibrous dysplasia, and café au lait pigmentation. Oral pigmentation is an underrecognized finding in MAS and presents later in development compared with the other mucosal lentiginosis syndromes. The diagnosis of MAS is most commonly a clinical diagnosis because mutational analysis is challenging in mosaic conditions. Expanding the cutaneous phenotype to include oral pigmentation further characterizes the clinical findings in this mosaic condition, broadens the differential diagnosis of syndromes with oral pigmentation, and in some cases may aid in earlier diagnosis of MAS.

De novo small supernumerary marker chromosomes detected on 143 000 consecutive prenatal diagnoses: chromosomal distribution, frequencies, and characterization combining molecular cytogenetics approaches

The risk of clinical consequences in prenatal cases with de novo small supernumerary marker chromosomes (sSMC), often in mosaic conditions, is not easy to predict, which results in difficulties in genetic counseling. In this study, we evaluated the frequency, the chromosomal origin, and the clinical indication of 104 de novo sSMC detected in a monocenter survey on the basis of 143,000 consecutive prenatal diagnoses, and we assessed the reliability of molecular cytogenetics technologies for sSMC characterization. We detected a de novo sSMC frequency of 0.072%. Its incidence in advanced maternal age group is statistically different from that found in maternal anxiety indication (<35 years old). A higher prevalence of mosaicism in chorionic villi sampling (CVS) than in amniotic fluids was also revealed related to confined placental mosaicisms. The risk of confirmation in amniotic fluids of mosaics previously revealed at CVS was 33.3%. No uniparental disomy conditions were found when imprinted chromosomes were involved in the occurrence of de novo sSMC. The majority of de novo sSMC were acrocentric derived-chromosomes, and a neocentromere formation was observed in one pregnancy. Our data support that array comparative genomic hybridization has improved sSMC characterization and demonstrate its utility in supporting genetic counseling. We propose a workflow for de novo sSMC characterization.

Molecular Diagnostics in Genodermatoses

In recent years, there has been tremendous progress in elucidating the molecular bases of genodermatoses. The interface between genetics and dermatology has broadened with the identification of "new" heritable disorders, improved recognition of phenotypic spectrums, and integration of molecular and clinical data to simplify disease categorization and highlight relationships between conditions. With the advent of next-generation sequencing and other technological advances, dermatologists have promising new tools for diagnosis of genodermatoses. This article first addresses phenotypic characterization and classification with the use of online databases, considering concepts of clinical and genetic heterogeneity. Indications for genetic testing related to medical care and patient/family decision making are discussed. Standard genetic testing is reviewed, including resources for finding specialized laboratories, methods of gene analysis, and patient/family counseling. The benefits and challenges associated with multigene panels, array-based analysis (eg, copy number variation, linkage, and homozygosity), and whole-exome or whole-genome sequencing are then examined. Specific issues relating to molecular analysis of mosaic skin conditions and prenatal/preimplantation diagnosis are also presented. Use of the modern molecular diagnostics described herein enhance our ability to counsel, monitor, and treat patients and families affected by genodermatoses, with broader benefits of providing insights into cutaneous physiology and multifactorial skin disorders.

Prenatal BACs‐on‐Beads™: a new technology for rapid detection of aneuploidies and microdeletions in prenatal diagnosis

Molecular cytogenetic techniques on uncultured prenatal samples are the sole tests applied in some countries in cases with advanced maternal age (AMA) or increased risk after prenatal screening. Moreover, there is a trend to perform invasive prenatal diagnosis (PD) during the first trimester before ultrasound manifestations, so new rapid and reliable assays are necessary to investigate microdeletions not detectable with the conventional karyotype. We report the validation study of the prenatal bacterial artificial chromosomes-on-Beads™ (BoBs™ ; CE-IVD), a bead-based multiplex assay detecting chromosomes 13, 18, 21, X/Y aneuploidies and nine microdeletion regions having an overall detection rate of 1/1700. We retrospectively studied 408 selected samples and prospectively tested 212 consecutive samples ascertained for conventional karyotyping. We did not find false-positive results. Triploidies were not detected. Maternal cell contamination of male samples up to 90% was unmasked inspecting gonosome profiles. Mosaic conditions at 20 to 30% were revealed. Failures were due to low amount of DNA. Prenatal BoBs™ is a robust technology for the investigation of fetuses with normal karyotype with or without sonographic abnormalities. Running in parallel with the karyotype analysis, it can be proposed instead of rapid FISH or QF-PCR providing rapid results on common aneuploidies and additional information regarding the microdeletion syndromes.