Tissue-specific Mosaicism Research Articles

A case report of Pallister-Killian syndrome with an unusual mosaic supernumerary marker chromosome 12 with interstitial 12p13.1-p12.1 duplication.

Pallister-Killian syndrome (PKS) is a rare inherited disease with multiple congenital anomalies, profound intellectual disability, and the presence in the karyotype of sSMC - i(12)(p10). The frequency of PKS may be underestimated due to problems with cytogenetic diagnosis caused by tissue-specific mosaicism and usually a low percentage of peripheral blood cells containing sSMC. Such tissue-specific mosaicism also complicates a detailed analysis of the sSMC, which, along with the assessment of mosaicism in different tissues, is an important part of cytogenetic diagnosis in PKS. Unfortunately, a full-fledged diagnosis in PKS is either practically impossible or complicated. On the one hand, this is due to problems with the biopsy of various tissues (skin biopsy with fibroblast culture is most often used in practice); on the other - a low percentage of dividing peripheral blood cells containing sSMC, which often significantly complicates the analysis of its composition and organization. In the present study, a detailed analysis of sSMC was carried out in a patient with a characteristic clinical picture of PKS. A relatively high percentage of peripheral blood cells with sSMC (50%) made it possible to perform a detailed molecular cytogenetic analysis of de novo sSMC using chromosomal in situ suppression hybridization (CISS-hybridization), multicolor FISH (mFISH), multicolor chromosome banding (MCB), array CGH (aCGH), and quantitative real-time PCR (qPCR), and short tandem repeat (STR) - analysis. As a result, it was found that the sSMC is not a typical PKS derivative of chromosome 12. In contrast to the classical i(12)(p10) for PKS, the patient's cells contained an acrocentric chromosome consisting of 12p material. Clusters of telomeric repeats were found at the both ends of the sSMC. Furthemore, the results of aCGH and qPCR indicate the presence of interstitial 8.9Mb duplication at 12p13.1-p12.1 within the sSMC, which leads to different representations of DNA from different segments of 12p within cells containing sSMC. The obtained data raise the question of the instability of the sSMC and, as a consequence, the possible presence of additional rearrangements, which, in traditional cytogenetic analysis of patients with PKS, are usually described as i(12)(p10).

Динамический тканеспецифичный мозаицизм кольцевой хромосомы 13

Кольцевая хромосома 13 является редкой структурной хромосомной аномалией. Изменение структуры хромосомы из линейной в кольцевую вызывает ее митотическую нестабильность, приводящую к соматическому динамическому мозаицизму вследствие которого формируются клоны клеток с различным вторичными числовыми и структурными хромосомными перестройками. Цитогеномный анализ культивированных лимфоцитов и фибробластов кожи в представленном случае кольцевой хромосомы 13 в кариотипе пациента с задержкой физического развития, микроцефалией и аномалиями развития выявил различную структуру вторичного геномного дисбаланса, вариабельный уровень динамического мозаицизма и избирательную эволюцию кариотипа. Ring chromosome 13 is a rare type of chromosome structural abnormalities. A change in the linear structure of the chromosome into a circular one causes its mitotic instability, leading to somatic dynamic mosaicism, which results in the formation of cell clones with various secondary numerical and structural chromosomal rearrangements. We report here a study on ring chromosome 13 instability in lymphocyte and fibroblast cultures established from a child with developmental delay, microcephaly and congenital abnormalities. The cytogenomic analysis revealed a different structure of secondary genomic imbalance, variable levels of dynamic mosaicism and selective karyotype evolution.

Searching chromosome mosaicisms in 45,X Turner syndrome: how relevant is it?

To investigate the presence of chromosome mosaicism, especially for the presence of Y derived material in 45,X women with Turner syndrome (TS). FISH and PCR were performed for the presence of chromosome mosaicism and Y-derived-material and genetic findings were correlated to clinical data. Thirty-one participants were enrolled: 18 (58%) had chromosome mosaicisms (FISH), Y-derived material was found in 2. Yet, SRY primer was found with PCR in only one of them and DYZ3 was not found. The most frequent clinical findings were short or webbed neck (81,82%), high-arched palate (78%), breast hypertelorism, e cubitus valgus and genu valgus (57.6%, both), short fourth metacarpals (46.9%), epicanthic folds (43.8%), shield chest (43.8%), lymphedema (37.5%), and low set ears (34.4%). Both patients with Y-derived-material had primary amenorrhea, dyslipidemia and reached the height of 150 cm despite not treated with recombinant growth hormone (GHr). One of them showed 26% of leukocytes with Y-derived material and few clinical findings. FISH techniques proved efficient in detecting chromosome mosaicisms and Y-derived material and searching in different tissues such as mouth cells is critical due to the possibility of tissue-specific mosaicism. Phenotypical variance in TS may be a signal of chromosome mosaicisms, especially with the presence of Y-derived material.

Causes and Consequences of Genome Instability in Psychiatric and Neurodegenerative Diseases

Each neuron has 100-10000 connections (synapses) with other neural cells, therefore genome pathologies affecting a small proportion of brain cells are capable of causing dysfunction of the entire central nervous system (CNS). Recently, genome and chromosome instability has been uncovered in neurodegeneration (Alzheimer's disease, ataxia telangiectasia). Somatic tissue-specific mosaicism was observed in the brain of individuals with neuropsychiatric diseases including schizophrenia, autism, intellectual disability, and epilepsy. The study of genetic processes in neurons allows determination of a certain number of genetic pathways and candidate processes, modifications of which can cause impaired genome stability. Brain-specific somatic mutations generally occur at the earliest stages of development. Accordingly, genome variability and somatic mosaicism are expected to be mediated by cell cycle regulation, DNA repair, DNA replication, and programmed cell death in the brain. Endomitosis, endoreduplication, and abortive entrance to the cell cycle are also commonly observed in neurodegeneration. Brain-specific genome instability maybe a key element in the pathogenic cascade of neurodegeneration. Here we review the current state of knowledge concerning somatic genome variations in neurodegenerative and psychiatric diseases and analyze the causes and consequences of genomic instability in the CNS.

Pathogenic copy number variants are detected in a subset of patients with gastrointestinal malformations.

BackgroundGastrointestinal atresias and urological defects are main causes of pediatric surgery in infants. As copy number variants (CNVs) have been shown to be involved in the development of congenital malformations, the aim of our study was to investigate the presence of CNVs in patients with gastrointestinal and urological malformations as well as the possibility of tissue‐specific mosaicism for CNVs in the cohort.MethodsWe have collected tissue and/or blood samples from 25 patients with anorectal malformations, esophageal atresia, or hydronephrosis, and screened for pathogenic CNVs using array comparative genomic hybridization (array‐CGH).ResultsWe detected pathogenic aberrations in 2/25 patients (8%) and report a novel possible susceptibility region for esophageal atresia on 15q26.3. CNV analysis in different tissues from the same patients did not reveal evidence of tissue‐specific mosaicism.ConclusionOur study shows that it is important to perform clinical genetic investigations, including CNV analysis, in patients with congenital gastrointestinal malformations since this leads to improved information to families as well as an increased understanding of the pathogenesis.

Implementation\xa0of a genomic medicine multi-disciplinary team approach for rare disease\xa0in the clinical setting: a prospective exome sequencing\xa0case series

BackgroundA multi-disciplinary approach to promote engagement, inform decision-making and support clinicians and patients is increasingly advocated to realise the potential of genome-scale sequencing in the clinic for patient benefit. Here we describe the results of establishing a genomic medicine multi-disciplinary team (GM-MDT) for case selection, processing, interpretation and return of results.MethodsWe report a consecutive case series of 132 patients (involving 10 medical specialties with 43.2% cases having a neurological disorder) undergoing exome sequencing over a 10-month period following the establishment of the GM-MDT in a UK NHS tertiary referral hospital. The costs of running the MDT are also reported.ResultsIn total 76 cases underwent exome sequencing following triage by the GM-MDT with a clinically reportable molecular diagnosis in 24 (31.6%). GM-MDT composition, operation and rationale for whether to proceed to sequencing are described, together with the health economics (cost per case for the GM-MDT was £399.61), the utility and informativeness of exome sequencing for molecular diagnosis in a range of traits, the impact of choice of sequencing strategy on molecular diagnostic rates and challenge of defining pathogenic variants. In 5 cases (6.6%), an alternative clinical diagnosis was indicated by sequencing results. Examples were also found where findings from initial genetic testing were reconsidered in the light of exome sequencing including TP63 and PRKAG2 (detection of a partial exon deletion and a mosaic missense pathogenic variant respectively); together with tissue-specific mosaicism involving a cytogenetic abnormality following a normal prenatal array comparative genomic hybridization.ConclusionsThis consecutive case series describes the results and experience of a multidisciplinary team format that was found to promote engagement across specialties and facilitate return of results to the responsible clinicians.

Tissue-specific mosaicism in a patient with Rubinstein-Taybi syndrome and CREBBP exon 1 duplication.

Tissue-specific mosaicism in a patient with Rubinstein-Taybi syndrome and CREBBP exon 1 duplication.

The impact of somatic mosaicism on bicuspid aortic valve and aortic dissection in Turner Syndrome.

Somatic mosaicism is a major modifier of turner syndrome (TS) features and may be more prevalent than once thought, as new molecular techniques enable detection of tissue-specific mosaicism. This review explores the causes of mosaicism, discusses how mosaicism may impact congenital aortic defects in TS, and summarizes molecular methods to detect mosaicism in different contexts.

Pallister-Killian syndrome: Review of fetal phenotype.

Pallister-Killian syndrome is a multi-system sporadic disorder with developmental delay. It is a rare chromosomal abnormality involving supernumerary isochormosome 12p. The disorder exhibits tissue specific mosaicism. The first prenatal diagnosis of PKS was reported in 1985 after ultrasound detection of fetal anomalies. Since this observation, there have been about 62 reports of fetuses with PKS. In this review, we cover the prenatal aspects of PKS.

Cytogenomic delineation and clinical follow-up of 10 Brazilian patients with Pallister-Killian syndrome.

BackgroundPallister-Killian syndrome (PKS) is a sporadic genetic disorder caused by the presence of a tissue-specific mosaicism for isochromosome 12p - i(12) (p10) and is characterized by facial dysmorphism including coarse facies, upslanting palpebral fissures, bitemporal alopecia, pigmentary skin anomalies, developmental delay, hypotonia and seizures. Although typical clinical features of PKS commonly exist, clinicians often do not raise the possibility of this diagnosis.ResultsWe reviewed the medical records of 10 patients with confirmed PKS followed in our service (since 1990 to 2015). Age at diagnosis varied from prenatal to 3 years and clinical features were consistent with those described in the literature. In all patients, peripheral blood karyotypes were normal and cytogenomic study was performed in order to confirm the diagnosis. Three of these patients had PKS diagnosis confirmed by buccal smear MLPA.ConclusionAn early conclusion from our results demonstrated that MLPA on buccal smears is a good and non-invasive method to detect extra copies of 12p and should be considered as the first exam, before a skin biopsy for a fibroblast karyotype is performed.

Mayer-Rokitansky-Küster-Hauser syndrome discordance in monozygotic twins: matrix metalloproteinase 14, low-density lipoprotein receptor–related protein 10, extracellular matrix, and neoangiogenesis genes identified as candidate genes in a tissue-specific mosaicism

To find a potential underlying cause for Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) discordance in monozygotic twins. Prospective comparative study. University hospital. Our study genetically analyzed 5 MRKHS-discordant monozygotic twin pairs with the unique opportunity to include saliva and rudimentary uterine tissue. Blood, saliva, or rudimentary uterine tissue from five MRKHS-discordant twins was analyzed and compared between twin pairs as well as within the same individual where applicable. We used copy number variations (CNVs) to identify differences. CNVs in blood, rudimentary uterine tissue, and saliva, network analysis, and review of the literature. One duplication found in the affected twin included two genes, matrix metalloproteinase 14 (MMP14) and low-density lipoprotein receptor-related protein 10 (LRP10), which have known functions in the embryonic development of the uterus and endometrium. The duplicated region was detected in rudimentary uterine tissue from the same individual but not in saliva, making a tissue-specific mosaicism a possible explanation for twin discordance. Additional network analysis revealed important connections to differentially expressed genes from previous studies. These genes encode several molecules involved in extracellular matrix (ECM) remodeling and neoangiogenesis. MMP-14, LRP-10, ECM, and neoangiogenesis genes are identified as candidate genes in a tissue-specific mosaicism. The detected clusters provide evidence of deficient vascularization during uterine development and/or disturbed reorganization of ECM components, potentially during müllerian duct elongation signaled by the embryologically relevant phosphatidylinositol 3-kinase/protein kinase B pathway.Therefore, we consider these genes to be new candidates in the manifestation of MRKHS.

In silico molecular cytogenetics: a bioinformatic approach to prioritization of candidate genes and copy number variations for basic and clinical genome research.

BackgroundThe availability of multiple in silico tools for prioritizing genetic variants widens the possibilities for converting genomic data into biological knowledge. However, in molecular cytogenetics, bioinformatic analyses are generally limited to result visualization or database mining for finding similar cytogenetic data. Obviously, the potential of bioinformatics might go beyond these applications. On the other hand, the requirements for performing successful in silico analyses (i.e. deep knowledge of computer science, statistics etc.) can hinder the implementation of bioinformatics in clinical and basic molecular cytogenetic research. Here, we propose a bioinformatic approach to prioritization of genomic variations that is able to solve these problems.ResultsSelecting gene expression as an initial criterion, we have proposed a bioinformatic approach combining filtering and ranking prioritization strategies, which includes analyzing metabolome and interactome data on proteins encoded by candidate genes. To finalize the prioritization of genetic variants, genomic, epigenomic, interactomic and metabolomic data fusion has been made. Structural abnormalities and aneuploidy revealed by array CGH and FISH have been evaluated to test the approach through determining genotype-phenotype correlations, which have been found similar to those of previous studies. Additionally, we have been able to prioritize copy number variations (CNV) (i.e. differentiate between benign CNV and CNV with phenotypic outcome). Finally, the approach has been applied to prioritize genetic variants in cases of somatic mosaicism (including tissue-specific mosaicism).ConclusionsIn order to provide for an in silico evaluation of molecular cytogenetic data, we have proposed a bioinformatic approach to prioritization of candidate genes and CNV. While having the disadvantage of possible unavailability of gene expression data or lack of expression variability between genes of interest, the approach provides several advantages. These are (i) the versatility due to independence from specific databases/tools or software, (ii) relative algorithm simplicity (possibility to avoid sophisticated computational/statistical methodology) and (iii) applicability to molecular cytogenetic data because of the chromosome-centric nature. In conclusion, the approach is able to become useful for increasing the yield of molecular cytogenetic techniques.

A mosaic maternal splice donor mutation in the EHMT1 gene leads to aberrant transcripts and to Kleefstra syndrome in the offspring

The euchromatic histone-lysine N-methyltransferase 1 (EHMT1) gene was examined in a 3-year-old boy with characteristic clinical features of Kleefstra syndrome. Sequencing of all 27 EHMT1 exons revealed a novel mutation, NM_024757.4:c.2712+1G>A, which affects the splice donor of intron 18. Whereas the index patient is heterozygous for that mutation, his phenotypically normal mother shows tissue-specific mosaicism. Sequencing of EHMT1 RT-PCR products revealed two aberrant transcript variants: in one variant, exon 18 was skipped; in the other, a near-by GT motif was used as splice donor and intronic sequence was inserted between exons 18 and 19. Both transcript variants were found in the patient and his mother. The latter had lower amounts of these transcripts consistent with mosaic status. This is the first description of an EHMT1 point mutation being inherited from a parent with verified mosaicism. The constitutive c.2712+1G>A splice site mutation in EHMT1 is fully pathogenic, and the transcript variants produced do not attenuate the severity of the disease.

Microarray comparative genomic hybridization and cytogenetic characterization of tissue‐specific mosaicism in three patients

The presence of more than one cell line in an individual may often be missed by classical cytogenetic analysis due to a low percentage of affected cells or analysis of cells from an unaffected or less affected germ layer. Array comparative genomic hybridization (aCGH) from whole blood or tissue is an important adjunct to standard karyotyping due to its ability to detect genomic imbalances that are below the resolution of karyotype analysis. We report results from three unrelated patients in whom aCGH revealed mosaicism not identified by peripheral blood chromosome analysis. This study further illustrates the important application of aCGH in detecting tissue-specific mosaicism, thereby leading to an improvement in the ability to provide a diagnosis for patients with normal chromosome analysis and dysmorphic features, congenital anomalies, and/or developmental delay.

Tissue‐specific mosaicism for tetrasomy 9p uncovered by array CGH

We report on a patient with a mild clinical phenotype, including genital anomalies, with mosaic tetrasomy 9p. Karyotype analysis of peripheral blood lymphocytes detected a supernumerary isochromosome 9p present in every cell, with the initial result being reported as tetrasomy 9p in non-mosaic form. However,array Comparative Genomic Hybridization (aCGH) studies on DNA extracted from peripheral blood lymphocytes and saliva showed that the patient had tissue-specific mosaicism, with a lower level of abnormal cells in the saliva. These results correlate with the patient's clinical features as non-mosaic cases of tetrasomy 9p have a more severe, often lethal, clinical phenotype. If non-mosaic tetrasomy 9p is identified in a peripheral blood culture then examination of a different tissue type should be undertaken. Array CGH may be used as an alternative to karyotype analysis to estimate the level of mosaicism, and may eliminate the need for invasive skin biopsy as samples such as buccal smear and saliva can be used. Array CGH is able to detect mosaicism, establish the euchromatic content of supernumerary marker chromosomes, and identify imbalances elsewhere in the genome allowing more accurate counselling and prognosis for patients.

Gene Structure Induced Epigenetic Modifications of pericarp color1 Alleles of Maize Result in Tissue-Specific Mosaicism

BackgroundThe pericarp color1 (p1) gene encodes for a myb-homologous protein that regulates the biosynthesis of brick-red flavonoid pigments called phlobahpenes. The pattern of pigmentation on the pericarp and cob glumes depends upon the allelic constitution at the p1 locus. p1 alleles have unique gene structure and copy number which have been proposed to influence the epigenetic regulation of tissue-specific gene expression. For example, the presence of tandem-repeats has been correlated with the suppression of pericarp pigmentation though a mechanism associated with increased DNA methylation.Methodology/Principal FindingsHerein, we extensively characterize a p1 allele called P1-mosaic (P1-mm) that has mosaic pericarp and light pink or colorless cob glumes pigmentation. Relative to the P1-wr (white pericarp and red cob glumes), we show that the tandem repeats of P1-mm have a modified gene structure containing a reduced number of repeats. The P1-mm has reduced DNA methylation at a distal enhancer and elevated DNA methylation downstream of the transcription start site.Conclusions/SignificanceMosaic gene expression occurs in many eukaryotes. Herein we use maize p1 gene as model system to provide further insight about the mechanisms that govern expression mosaicism. We suggest that the gene structure of P1-mm is modified in some of its tandem gene repeats. It is known that repeated genes are susceptible to chromatin-mediated regulation of gene expression. We discuss how the modification to the tandem repeats of P1-mm may have disrupted the epigenetic mechanisms that stably confer tissue-specific expression.

Ring syndrome: still true?

We thank Zollino et al for giving us the opportunity to discuss the ring syndrome and its related short stature. According to Cote et al 1 and Kosztolanyi,2 ring syndrome...

The Pallister-Killian syndrome in a child with rare karyotype—a diagnostic problem

The Pallister-Killian syndrome is a clinically recognizable syndrome, usually due to a tissue-specific mosaicism for a 12p isochromosome [i(12p)]. We report a rare case of Pallister-Killian syndrome with 12p mosaicism, tetrasomy/trisomy/disomy in fibroblasts and trisomy/disomy in lymphocytes. Marker chromosomes were investigated with conventional cytogenetic techniques and fluorescent in situ hybridisation (FISH). The karyotype was established as: mos47,XX,+12p/47,XX,+i(12p)/46,XX. The cytogenetic result of the extra mosaic 12p presented in lymphocytes suggested the diagnosis of trisomy 12p, although, in combination with clinical manifestations, the Pallister-Killian syndrome was considered and confirmed by the cytogenetic analysis of fibroblasts.

Pallister-Killian Syndrome: Rapid Decrease of Isochromosome 12p Frequency during Amniocyte Subculturing. Conclusion for Strategy of Prenatal Cytogenetic Diagnostics

Pallister-Killian syndrome (PKS) is characterized cytogenetically by mosaic tetrasomy of chromosome 12p. Routine prenatal diagnosis of PKS is still complicated because of the difficulties of discriminating between the supernumerary isochromosome 12p and the duplication 21q and because of the variable level of mosaicism. The frequency of cells with an extra metacentric chromosome i(12)(p10) is usually determined by tissue-limited or tissue-specific mosaicism. We demonstrated a decrease of the abnormal clone with extra i(12p) in the amniotic fluid cells of the PKS fetus during amniocyte subculturing. The rapid loss of the i(12p) in the course of amniocyte subculturing should be the focus of attention during prenatal karyotyping. This is especially necessary for cultures with slow growth, which require further interpretation of the result during cytogenetic diagnosis of PKS.

MSH2-dependent germinal CTG repeat expansions are produced continuously in spermatogonia from DM1 transgenic mice.

Myotonic dystrophy type 1 is a neuromuscular affection associated with the expansion of an unstable CTG repeat in the DM protein kinase gene. The disease is characterized by somatic tissue-specific mosaicism and very high intergenerational instability with a strong bias towards expansions. We used transgenic mice carrying more than 300 unstable CTG repeats within their large human genomic environment to investigate the dynamics of CTG repeat germinal mosaicism in males. Germinal mosaicism towards expansions was already present in spermatozoa at 7 weeks of age and continued to increase with age, suggesting that expansions are continuously produced throughout life. To determine the precise stage at which germinal expansions occur during spermatogenesis, we sorted and collected the different germ cell types produced during spermatogenesis from males of different ages and analyzed the CTG repeat mosaicism in each fraction. Strong mosaicisms towards expansions were already observed in spermatogonia before meiosis. In transgenic Msh2-deficient mice, germinal instability of the CTG repeats (only contractions) also occurs premeiotically. No significant difference in mosaicism was detected between spermatogonia and spermatozoa, arguing against continued expansions during postmeiotic stages. This indicates that germinal expansions are produced at the beginning of spermatogenesis, in spermatogonia, by a meiosis-independent mechanism involving MSH2.