Journal articles: 'Cryptic Mosaicism'

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Čulić, Vida, Ruzica Lasan-Trcić, Thomas Liehr, Igor N. Lebedev, Maja Pivić, Jasminka Pavelic, and Robert Vulić. "A Familial Small Supernumerary Marker Chromosome 15 Associated with Cryptic Mosaicism with Two Different Additional Marker Chromosomes Derived de novo from Chromosome 9: Detailed Case Study and Implications for Recurrent Pregnancy Loss." Cytogenetic and Genome Research 156, no. 4 (2018): 179–84. http://dx.doi.org/10.1159/000494822.

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We report a case of familial small supernumerary marker chromosome 15 in a phenotypically normal female with 4 recurrent spontaneous abortions and a healthy child. The initial karyotype showed a small, bisatellited, apparently metacentric marker chromosome, 47,XX,+idic(15)(q11.1), maternally inherited. The proband's mother was mosaic for the idic(15)(q11.1) without pregnancy loss. Reexamination of the proband's karyotype revealed cryptic mosaicism for 1 ring and 1 minute chromosome derived de novo from chromosome 9 in 2% of the metaphases. In FISH analysis, the patient's karyotype was mos 47,XX,+idic(15)(q11.1)mat[100]/49,XX,+idic(15)(q11.1)mat,+r(9;9;9;9),+der(9)dn[2]. The second spontaneous abortion had trisomy 9 (47,XX,+9); the third had mosaic trisomy 9 in 21% of the nuclei and isodicentric chromosome 15 in 36% of the nuclei (mos 48,XN,+9,+idic(15)(q11.1)/47,XN,+9/47,XN,+idic(15)(q11.1)/46,XN). The first and fourth abortions were not cytogenetically studied. The cause of the spontaneous abortions in this patient is likely the cryptic mosaicism for ring and minute chromosomes 9, and gonadal mosaicism is most probable, due to the 2 abortions.

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Dupont, Celine, Andree Delahaye, Lydie Burglen, Anne-Claude Tabet, Azzedine Aboura, Samia Kanafani, Françoise Baverel, Thierry Billette de Villemeur, Brigitte Benzacken, and Eva Pipiras. "First cryptic balanced reciprocal translocation mosaicism and familial transmission." American Journal of Medical Genetics Part A 146A, no. 22 (November 15, 2008): 2971–74. http://dx.doi.org/10.1002/ajmg.a.32547.

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Stefanou, E.-G., M. Crocker, A. Boon, and H. Stewart. "Cryptic mosaicism for monosomy 20 identified in renal tract cells." Clinical Genetics 70, no. 3 (July 12, 2006): 228–32. http://dx.doi.org/10.1111/j.1399-0004.2006.00652.x.

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Aliaga, Solange M., Howard R. Slater, David Francis, Desiree Du Sart, Xin Li, David J. Amor, Angelica M. Alliende, et al. "Identification of Males with Cryptic Fragile X Alleles by Methylation-Specific Quantitative Melt Analysis." Clinical Chemistry 62, no. 2 (February 1, 2016): 343–52. http://dx.doi.org/10.1373/clinchem.2015.244681.

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Abstract BACKGROUND FMR1 full mutations (FMs) (CGG expansion >200) in males mosaic for a normal (<45 CGG) or gray-zone (GZ) (45–54 CGG) allele can be missed with the standard 2-step fragile X syndrome (FXS) testing protocols, largely because the first-line PCR tests showing a normal or GZ allele are not reflexed to the second-line test that can detect FM. METHODS We used methylation-specific quantitative melt analysis (MS-QMA) to determine the prevalence of cryptic FM alleles in 2 independent cohorts of male patients (994 from Chile and 2392 from Australia) referred for FXS testing from 2006 to 2013. All MS-QMA–positive cases were retested with commercial triplet primed PCR, methylation-sensitive Southern blot, and a methylation-specific EpiTYPER-based test. RESULTS All 38 FMs detected with the standard 2-step protocol were detected with MS-QMA. However, MS-QMA identified methylation mosaicism in an additional 15% and 11% of patients in the Chilean and Australian cohorts, respectively, suggesting the presence of a cryptic FM. Of these additional patients, 57% were confirmed to carry cryptic expanded alleles in blood, buccal mucosa, or saliva samples. Further confirmation was provided by identifying premutation (CGG 55–199) alleles in mothers of probands with methylation-sensitive Southern blot. Neurocognitive assessments showed that low-level mosaicism for cryptic FM alleles was associated with cognitive impairment or autism. CONCLUSIONS A substantial number of mosaic FM males who have cognitive impairment or autism are not diagnosed with the currently recommended 2-step testing protocol and can be identified with MS-QMA as a first-line test.

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Daniel, Art, Zhanhe Wu, Artur Darmanian, Paul Malafiej, Varsha Tembe, Greg Peters, Craig Kennedy, and Lesley Adès. "Issues arising from the prenatal diagnosis of some rare trisomy mosaics—the importance of cryptic fetal mosaicism." Prenatal Diagnosis 24, no. 7 (July 2004): 524–36. http://dx.doi.org/10.1002/pd.936.

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McDonough, Paul G., and Sandra P. T. Tho. "Clinical implications of overt and cryptic Y mosaicism in individuals with dysgenetic gonads." International Congress Series 1298 (October 2006): 13–20. http://dx.doi.org/10.1016/j.ics.2006.06.011.

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Bispo, Adriana Valéria Sales, Pollyanna Burégio-Frota, Luana Oliveira dos Santos, Gabriela Ferraz Leal, Andrea Rezende Duarte, Jacqueline Araújo, Vanessa Cavalcante da Silva, Maria Tereza Cartaxo Muniz, Thomas Liehr, and Neide Santos. "Y chromosome in Turner syndrome: detection of hidden mosaicism and the report of a rare X;Y translocation case." Reproduction, Fertility and Development 26, no. 8 (2014): 1176. http://dx.doi.org/10.1071/rd13207.

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Turner syndrome (TS) is a common genetic disorder in females associated with the absence of complete or parts of a second sex chromosome. In 5–12% of patients, mosaicism for a cell line with a normal or structurally abnormal Y chromosome is identified. The presence of Y-chromosome material is of medical importance because it results in an increased risk of developing gonadal tumours and virilisation. Molecular study and fluorescence in situ hybridisation approaches were used to study 74 Brazilian TS patients in order to determine the frequency of hidden Y-chromosome mosaicism, and to infer the potential risk of developing malignancies. Additionally, we describe one TS girl with a very uncommon karyotype 46,X,der(X)t(X;Y)(p22.3?2;q11.23) comprising a partial monosomy of Xp22.3?2 together with a partial monosomy of Yq11.23. The presence of cryptic Y-chromosome-specific sequences was detected in 2.7% of the cases. All patients with Y-chromosome-positive sequences showed normal female genitalia with no signs of virilisation. Indeed, the clinical data from Y-chromosome-positive patients was very similar to those with Y-negative results. Therefore, we recommend that the search for hidden Y-chromosome mosaicism should be carried out in all TS cases and not be limited to virilised patients or carriers of a specific karyotype.

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Murdock, David R., Frank X. Donovan, Settara C. Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, and Paul Kruszka. "Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening." Journal of Clinical Endocrinology & Metabolism 102, no. 5 (January 24, 2017): 1529–37. http://dx.doi.org/10.1210/jc.2016-3414.

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Abstract Context: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in female patients and is not currently part of newborn screening (NBS). Diagnosis is often delayed, resulting in missed crucial diagnostic and therapeutic opportunities. Objectives: This study sought to determine if whole-exome sequencing (WES) as part of a potential NBS program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on blood samples from women with TS (n = 27) enrolled in the Personalized Genomic Research study at the National Institutes of Health. Female control subjects (n = 37) and male subjects (n = 27) also underwent WES. Copy number variation was evaluated using EXCAVATOR2 and B allele frequency was calculated from informative single nucleotide polymorphisms. Simulated WES data were generated for detection of low-level mosaicism and complex structural chromosome abnormalities. Results: We detected monosomy for chromosome X in all 27 TS samples, including 1 mosaic for 45,X/46,XX and another with previously unreported material on chromosome Y. Sensitivity and specificity were both 100% for the diagnosis of TS with no false-positive or false-negative results. Using simulated WES data, we detected isochromosome Xq and low-level mosaicism as low as 5%. Conclusion: We present an accurate method of diagnosing TS using WES, including cases with low-level mosaicism, isochromosome Xq, and cryptic Y-chromosome material. Given the potential use of next-generation sequencing for NBS in many different diseases and syndromes, we propose WES can be used as a screening test for TS in newborns.

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Pinto, Anna Maria, Sergio Daga, Chiara Fallerini, Mirella Bruttini, Margherita Baldassarri, Annarita Giliberti, Elisa Frullanti, Andrea Guarnieri, Guido Garosi, and Alessandra Renieri. "Detection of Cryptic Mosaicism in X-linked Alport Syndrome Prompts to Re-evaluate Living-donor Kidney Transplantation." Transplantation 104, no. 11 (December 31, 2019): 2360–64. http://dx.doi.org/10.1097/tp.0000000000003104.

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Kim, Jin Woo, Eun Hee Cho, Young Mi Kim, Jin Mee Kim, Jung Yeol Han, and So Yeon Park. "Detection of cryptic Y chromosome mosaicism by coamplification PCR with archived cytogenetic slides of suspected Turner syndrome." Experimental & Molecular Medicine 32, no. 1 (March 2000): 38–41. http://dx.doi.org/10.1038/emm.2000.7.

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Ballif, Blake C., Christina J. Ramirez, Casey R. Carl, Kyle Sundin, Melissa Krug, Adam Zahand, Lisa G. Shaffer, and Helen Flores-Smith. "The PMEL Gene and Merle in the Domestic Dog: A Continuum of Insertion Lengths Leads to a Spectrum of Coat Color Variations in Australian Shepherds and Related Breeds." Cytogenetic and Genome Research 156, no. 1 (2018): 22–34. http://dx.doi.org/10.1159/000491408.

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Merle is a distinct coat color and pattern found in numerous species, including the domestic dog, characterized by patches of diluted eumelanin (black pigment) interspersed among areas of normal pigmentation. In dogs, this variegated pattern is caused by an insertion of a SINE element into the canine PMEL gene. Although variation in the length of the SINE insertion - due to a variable-length poly(A) tail - has been observed to be associated with variation in merle coat color and patterning, no systematic evaluation of this correlation has been conducted and published in the scientific literature. We performed high-resolution analysis of the SINE insertion lengths in 175 dogs (99 Australian shepherds, 45 miniature Australian shepherds, and 31 miniature American shepherds) and compared the genotypes with the coat phenotypes (when available). SINE insertion lengths varied from 201 to 277 bp, indicating that merle insertion variants can occur in virtually any size along the entire continuum. Genotype-phenotype correlation of 126 dogs with only a single SINE insertion (m/M) identified at least 4 major phenotypic clusters designated as “cryptic,” “atypical,” “classic,” and “harlequin” merle. However, we found several phenotypic outliers that did not cluster within these major groupings, suggesting that insertion size is not the only factor responsible for merle phenotypic variability. In addition, we detected 25 dogs with 2 SINE insertions (M/M) and 24 dogs with more than 2 PMEL (merle) alleles, indicating mosaicism. Genotype-phenotype correlation of M/M dogs suggests that cryptic merle alleles often act like non-merle (m) alleles when combined with atypical, classic, and harlequin-sized alleles. The finding of mosaicism has important implications for the dog's phenotype and the ability to potentially transmit various alleles to its offspring. Furthermore, we identified examples of the SINE insertion poly(A)-tail expansion and contraction between generations, which also has important implications for breeding practices and determining mating pairs to avoid producing double merle dogs. These data demonstrate that there is a continuum of merle insertion lengths associated with a spectrum of coat color and patterns and that genotype-phenotype exceptions and overlap make it difficult to strictly assign certain insertion sizes with an expected coat color, although some generalizations are possible.

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Gijsbers, Antoinet C. J., Johannes G. Dauwerse, Cathy A. J. Bosch, Elles M. J. Boon, Wilco van den Ende, Sarina G. Kant, Kerstin M. B. Hansson, Martijn H. Breuning, Egbert Bakker, and Claudia A. L. Ruivenkamp. "Three new cases with a mosaicism involving a normal cell line and a cryptic unbalanced autosomal reciprocal translocation." European Journal of Medical Genetics 54, no. 4 (July 2011): e409-e412. http://dx.doi.org/10.1016/j.ejmg.2011.05.002.

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Gökpınar İli, Ezgi, Şule Altıner, and Halil G. Karabulut. "Cytogenetic, Molecular, and Phenotypic Characterization of a Patient with de novo Derivative Chromosome 18 and Review of the Literature." Cytogenetic and Genome Research 159, no. 2 (2019): 74–80. http://dx.doi.org/10.1159/000503574.

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We present a patient with a de novo derivative chromosome 18 which includes a terminal deletion of 18p and a terminal duplication of 18q accompanied by a cryptic duplication of 18p. The girl had mild dysmorphic features such as micro-retrognathia, upslanted palpebral fissures, bilateral epicanthus, high palate, low-set ears, short neck, and full cheeks. She also had an H-type tracheoesophageal fistula which required surgery. Her cognitive and motor skills were delayed. Karyotype analysis showed an additional segment on the short arm of chromosome 18. Chromosomal microarray revealed a 7.3-Mb terminal loss from 18p11.32 to 18p11.23, a 22.2-Mb terminal gain from 18q21.31 to 18q23, and a 3.9-Mb interstitial gain from 18p11.22 to 18p11.21. We hypothesize that the mother has gonadal mosaicism for normal chromosome 18, der(18)dup(p11.22p11.21), and der(18)dup(p11. 22p11.21)inv(18)(p11.22q21.31), or both the terminal del/dup and the interstitial duplication occurred simultaneously.

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Wise, Jasen L., Richard J. Crout, Daniel W. McNeil, Robert J. Weyant, Mary L. Marazita, and Sharon L. Wenger. "Cryptic Subtelomeric Rearrangements and X Chromosome Mosaicism: A Study of 565 Apparently Normal Individuals with Fluorescent In Situ Hybridization." PLoS ONE 4, no. 6 (June 10, 2009): e5855. http://dx.doi.org/10.1371/journal.pone.0005855.

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Vulliamy, T. J., S. W. Knight, N. S. Heiss, O. P. Smith, A. Poustka, I. Dokal, and P. J. Mason. "Dyskeratosis Congenita Caused by a 3′ Deletion: Germline and Somatic Mosaicism in a Female Carrier." Blood 94, no. 4 (August 15, 1999): 1254–60. http://dx.doi.org/10.1182/blood.v94.4.1254.

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Abstract X-linked dyskeratosis congenita (DC) is a bone marrow failure syndrome caused by mutations in the DKC1 gene located at Xq28. By 20 years of age, most affected boys develop bone marrow failure, whereas female carriers show a skewed pattern of X-chromosome inactivation. The gene product, dyskerin, is homologous to a yeast protein involved in ribosomal RNA biogenesis, providing a unique insight into a cause of aplastic anemia. Whereas most causative mutations are single amino acid substitutions, and nonsense or frameshift mutations have not been observed, we present here a case of DC caused by a 2-kb deletion that removes the last exon of the gene. Normal levels of mRNA are produced from the deleted gene, with the transcripts using a cryptic polyadenylation site in the antisense strand of the adjacent MPP1 gene, normally located 1 kb downstream of DKC1 in a tail to tail orientation. The predicted truncated protein lacks a lysine-rich peptide that is less conserved than the rest of the dyskerin molecule and is dispensable in yeast, supporting the contention that it may retain some activity and that null mutations at this locus may be lethal. The affected boy had an unaffected brother with the same haplotype around the DKC1 gene and a sister who was heterozygous for the deletion. We conclude therefore that the mother must be a germline mosaic with respect to this deletion. Investigation of her blood cells and other somatic tissues showed that a small proportion of these cells also carried the deletion, making her a somatic mosaic and indicating that the deletion took place early in development.

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Vulliamy, T. J., S. W. Knight, N. S. Heiss, O. P. Smith, A. Poustka, I. Dokal, and P. J. Mason. "Dyskeratosis Congenita Caused by a 3′ Deletion: Germline and Somatic Mosaicism in a Female Carrier." Blood 94, no. 4 (August 15, 1999): 1254–60. http://dx.doi.org/10.1182/blood.v94.4.1254.416k24_1254_1260.

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X-linked dyskeratosis congenita (DC) is a bone marrow failure syndrome caused by mutations in the DKC1 gene located at Xq28. By 20 years of age, most affected boys develop bone marrow failure, whereas female carriers show a skewed pattern of X-chromosome inactivation. The gene product, dyskerin, is homologous to a yeast protein involved in ribosomal RNA biogenesis, providing a unique insight into a cause of aplastic anemia. Whereas most causative mutations are single amino acid substitutions, and nonsense or frameshift mutations have not been observed, we present here a case of DC caused by a 2-kb deletion that removes the last exon of the gene. Normal levels of mRNA are produced from the deleted gene, with the transcripts using a cryptic polyadenylation site in the antisense strand of the adjacent MPP1 gene, normally located 1 kb downstream of DKC1 in a tail to tail orientation. The predicted truncated protein lacks a lysine-rich peptide that is less conserved than the rest of the dyskerin molecule and is dispensable in yeast, supporting the contention that it may retain some activity and that null mutations at this locus may be lethal. The affected boy had an unaffected brother with the same haplotype around the DKC1 gene and a sister who was heterozygous for the deletion. We conclude therefore that the mother must be a germline mosaic with respect to this deletion. Investigation of her blood cells and other somatic tissues showed that a small proportion of these cells also carried the deletion, making her a somatic mosaic and indicating that the deletion took place early in development.

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Santos, M., K. Mrasek, I. Madrigal, M. R. Martorell, A. González-Meneses, G. Rodríguez-Criado, M. Milà, T. Liehr, and C. Fuster. "Characterization of a complex cryptic mosaicism for an sSMC derived from the X chromosome present in a boy with congenital malformations." American Journal of Medical Genetics Part A 152A, no. 10 (September 2, 2010): 2661–63. http://dx.doi.org/10.1002/ajmg.a.33638.

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Santos, Mònica, Kristin Mrasek, Maria Àngels Rigola, Heike Starke, Thomas Liehr, and Carme Fuster. "Identification of a “cryptic mosaicism” involving at least four different small supernumerary marker chromosomes derived from chromosome 9 in a woman without reproductive success." Fertility and Sterility 88, no. 4 (October 2007): 969.e11–969.e17. http://dx.doi.org/10.1016/j.fertnstert.2006.12.073.

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Stabile, M., T. Angelino, F. Caiazzo, P. Olivieri, N. De Marchi, L. De Petrocellis, and P. Orlando. "Fertility in a i(Xq) Klinefelter patient: importance of XIST expression level determined by qRT-PCR in ruling out Klinefelter cryptic mosaicism as cause of oligozoospermia." Molecular Human Reproduction 14, no. 11 (October 14, 2008): 635–40. http://dx.doi.org/10.1093/molehr/gan057.

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Pandelache, Alison, David Francis, Ralph Oertel, Rebecca Dickson, Rani Sachdev, Ling Ling, Dinusha Gamage, and David E. Godler. "Detection of Cryptic Fragile X Full Mutation Alleles by Southern Blot in a Female and Her Foetal DNA via Chorionic Villus Sampling, Complicated by Mosaicism for 45,X0/46,XX/47,XXX." Genes 12, no. 6 (May 24, 2021): 798. http://dx.doi.org/10.3390/genes12060798.

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We describe a female with a 72 CGG FMR1 premutation (PM) (CGG 55–199) and family history of fragile X syndrome (FXS), referred for prenatal testing. The proband had a high risk of having an affected pregnancy with a full mutation allele (FM) (CGG > 200), that causes FXS through hypermethylation of the FMR1 promoter. The CGG sizing analysis in this study used AmplideX triplet repeat primed polymerase chain reaction (TP-PCR) and long-range methylation sensitive PCR (mPCR). These methods detected a 73 CGG PM allele in the proband’s blood, and a 164 CGG PM allele in her male cultured chorionic villus sample (CVS). In contrast, the Southern blot analysis showed mosaicism for: (i) a PM (71 CGG) and an FM (285–768 CGG) in the proband’s blood, and (ii) a PM (165 CGG) and an FM (408–625 CGG) in the male CVS. The FMR1 methylation analysis, using an EpiTYPER system in the proband, showed levels in the range observed for mosaic Turner syndrome. This was confirmed by molecular and cytogenetic karyotyping, identifying 45,X0/46,XX/47,XXX lines. In conclusion, this case highlights the importance of Southern blot in pre- and postnatal testing for presence of an FM, which was not detected using AmplideX TP-PCR or mPCR in the proband and her CVS.

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Capkova, Pavlina, Zuzana Capkova, Peter Rohon, Katerina Adamová, and Jirina Zapletalova. "Short stature and SHOX (Short stature homeobox) variants—efficacy of screening using various strategies." PeerJ 8 (November 17, 2020): e10236. http://dx.doi.org/10.7717/peerj.10236.

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Background SHOX mutations have previously been described as causes of Léri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), and idiopathic short stature. The loss of X chromosome—Turner syndrome or mosaic 45,X/46,XX or 46,XY—also leads to the heterozygous loss of SHOX in patients with short stature only or with features similar to LWD. The aim of this study was to assess the efficacy of the targeted screening for SHOX variants, which involved different methods in the laboratory analysis of short stature. We determined the significance and positive predictive value of short stature for the detection of SHOX variants. Methods Targeted screening for variants in SHOX involving MLPA, sequencing, karyotyping and FISH was performed in the short stature cohort (N = 174) and control cohort (N = 91). The significance of short stature and particular characteristics for the detection of SHOX variants was determined by Fisher’s exact test, and the probability of SHOX mutation occurrence was calculated using a forward/stepwise logistic regression model. Results In total, 27 and 15 variants influencing SHOX were detected in the short stature and control cohorts, respectively (p > 0.01). Sex chromosome aberrations and pathogenic CNV resulting in diagnosis were detected in eight (4.6%) and five (2.9%) patients of the short stature group and three (3.3%) and one (1.1%) individuals of the control group. VUS variants were discovered in 14 (8.0%) and 11 (12.1%) individuals of the short stature and control groups, respectively. MLPA demonstrated the detection rate of 13.22%, and it can be used as a frontline method for detection of aberrations involving SHOX. However, only mosaicism of monosomy X with a higher frequency of monosomic cells could be reliably discovered by this method. Karyotyping and FISH can compensate for this limitation; their detection rates in short stature group were 3.55% and 13.46% (N = 52), respectively. FISH proved to be more effective than karyotyping in the study as it could reveal cryptic mosaics in some cases where karyotyping initially failed to detect such a clone. We suggest adding FISH on different tissue than peripheral blood to verify sex-chromosome constitution, especially in cases with karyotypes: 45,X; mosaic 45,X/46,XX or 46,XY; 46,Xidic(Y) detected from blood; in children, where mosaic 45,X was detected prenatally but was not confirmed from peripheral blood. The correlation of short stature with the occurrence of SHOX mutations was insignificant and short stature demonstrates a low positive predictive value-15.5% as unique indicator for SHOX mutations. The typical skeletal signs of LWD, including Madelung deformity and disproportionate growth, positively correlate with the findings of pathogenic SHOX variants (p < 0.01) by Fisher’s exact test but not with the findings of VUS variants in SHOX which are more prevalent in the individuals with idiopathic short stature or in the individuals with normal height.

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Iacucci, M., E. Grisan, N. Labarile, O. Nardone, S. C. Smith, L. Jeffery, S. Ghosh, and A. Buda. "P397 Response to biologics in IBD patients assessed by Computerized image analysis of Probe Based Confocal Laser Endomicroscopy with molecular labeling." Journal of Crohn's and Colitis 15, Supplement_1 (May 1, 2021): S406—S407. http://dx.doi.org/10.1093/ecco-jcc/jjab076.521.

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Abstract Background The increase in therapeutic choices in inflammatory bowel diseases (IBD) imposed the identification of personalized therapeutic strategy. Confocal laser endomicroscopy (CLE) is a new endoscopic tool developed to obtain virtual in vivo histology. This study aimed to identify CLE in vivo and ex vivo features predictive of response for patients starting biologics. Methods We performed a prospective observational study at a single tertiary referral centre. 29 IBD patients (14 ulcerative colitis-UC and 15 Crohn’s Disease-CD) underwent colonoscopy with CLE before and 12-14 weeks after starting anti -TNF or 16 weeks after anti α4β7 integrin. CLE parameters analyzed were: crypt distribution along the mucosal surface, crypt area (CA), eccentricity, diameter, inter-cryptic distance (ICD), vessel tortuosity (VT), fluorescein leakage through the colonic mucosa (FLCM). Ex-vivo binding activity of fluorescein labelled biologics on corresponding biopsies was also assessed. Mosaicism reconstruction of CLE images were analyzed using a dedicated software algorithm (CellvizioViewer, Mauna Kea Technologies, ParisFrance). A dedicated Graphical User Interface was designed to enable a semiautomated analysis. Results After treatment, VT resulted significantly changed in overall IBD population (p<0.05), FLCM were reduced in UC patients (p<0.05), whilst CA, eccentricity and ICD decreased in CD patients (p< 0.05). The univariate regression analysis identified FLCM as the most accurate parameter for predicting responsiveness (AUROC) 83%, accuracy 83%, positive predictive value-PPV 94% and negative predictive value-NPV 57%). FLCM and ICD were the best discriminants in responders Vs non responders in UC patients (AUROC 85%, accuracy 85%, PPV 100% and NPV 71%); whilst VT, CA and ICD in CD patients (AUROC 95%, 86% and 83%; accuracy 90%, 90% and 88%; PPV 100%, 100% and 86%; and NPV 75%, 75% and 100%, respectively). Ex vivo confocal imaging revealed that UC patients, especially those responders, had higher basal fluorescent intensity signals with a significant reduction after biological treatment (p< 0.05), whereas in CD patients no significant change was found. An increased mucosal binding to the fluorescent labelled biological agent was associated to a higher likelihood of response to the treatment; this effect was higher in UC patients (AUROC 81%, accuracy 77%, PPV 100%, NPV 63%) compared to CD patients (AUROC 64%, accuracy 79%, PPV 80%, NPV 50%). Conclusion FLCM and ICD were the best discriminants of response in UC, while VT, CA and ICD in CD. A higher mucosal binding to a biological agent before treatment was observed in responders UC patients but not in CD patients.

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Martin, Guillaume, Céline Cardi, Gautier Sarah, Sébastien Ricci, Christophe Jenny, Emmanuel Fondi, Xavier Perrier, Jean‐Christophe Glaszmann, Angélique D'Hont, and Nabila Yahiaoui. "Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana." Plant Journal 102, no. 5 (February 28, 2020): 1008–25. http://dx.doi.org/10.1111/tpj.14683.

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О.А., Соловова,, Опарина, Н.В., Сорокина, Т.М., Андреева, М.В., Хаят, С.Ш., Штаут, М.И., Коталевская, Ю.Ю., et al. "Comprehensive genetic examination of azoospermiс and severe oligozoospermiс patients." Nauchno-prakticheskii zhurnal «Medicinskaia genetika, no. 12 (December 27, 2021): 12–22. http://dx.doi.org/10.25557/2073-7998.2021.12.12-22.

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Введение. Тяжелые формы нарушения репродукции часто связаны с генетическими факторами. Однако по ряду причин медико-генетическое обследование и консультирование пациентов с бесплодием недостаточно эффективны, и вклад многих генетических факторов в генез нарушения фертильности остается недостаточно изученным. Комплексный подход к обследованию с использованием различных клинических, цитогенетических и молекулярно-генетических методов позволяет улучшить диагностику генетически обусловленных форм нарушения фертильности, в частности связанных с азооспермией или олигозооспермией тяжелой степени. Цель: повышение эффективности медико-генетического обследования и консультирования пациентов с азооспермией и олигозооспермией. Методы. В отобранную выборку включены 200 мужчин с азооспермией (n=172) и олигозооспермией тяжелой степени (n=28). Пациентам выполнено клиническое, андрологическое и лабораторно-инструментальное обследование: УЗИ органов мошонки, сперматологическое, гормональное, цитогенетическое, молекулярно-цитогенетическое (FISH) и молекулярно-генетическое исследования локусов или генов, связанных с нарушением мужской фертильности (AZF, гены CFTR, AR). Результаты. Различные генетические факторы нарушения фертильности обнаружены у 99 (49,5%) из 200 пациентов, в том числе у 76 (45,7%) мужчин с азооспермией и у 23 (82,1%) пациентов с олигозооспермией. Муковисцидоз и синдром CBAVD диагностированы у 4,5% пациентов, врожденный гипогонадотропный гипогонадизм - у 7,5% мужчин. Аномалии кариотипа обнаружены у 52 (26,8%) пациентов, включая синдром Клайнфельтера (47,XXY; n=34), дисомию Y (47,XYY; n=6), 46,XX тестикулярную форму нарушения формирования пола (n=3), сбалансированные аномалии аутосом (n=9). По результатам FISH-анализа у пациентов c анеуплоидией по половым хромосомам не обнаружено скрытого мозаицизма. Патогенные микроделеции Y-хромосомы в локусе AZF (Yq11.2) обнаружены у 16 (8%) пациентов. Патогенные варианты в гене CFTR детектированы у 9 пациентов с муковисцидозом и синдромом CBAVD. Выводы. Использование комплексного генетического обследования позволяет существенно повысить эффективность диагностики генетически обусловленных форм мужского бесплодия, связанного с тяжелыми формами патозооспермии. Для выявления редких несиндромальных генетических форм нарушения фертильности, связанных с генными вариантами и вариациями числа копий, необходимо применение массового параллельного секвенирования, хромосомного микроматричного анализа и других методов геномного анализа. Background. Severe forms of reproduction disorders are often associated with genetic factors. However, for a number of reasons, medical and genetic examination and counseling of infertile patients are not effective enough, and the contribution of many genetic factors to the genesis of fertility disorders remains insufficiently studied. An integrated approach using various clinical, cytogenetic and molecular genetic methods in the examination makes it possible to improve the diagnosis of genetically determined forms of fertility disorders, in particular those associated with severe azoospermia or oligozoospermia. Aim: improving the effectiveness of medical and genetic examination and counseling of patients with severe azoospermia and oligozoospermia. Methods. The selected sample included 200 men with azoospermia (n=172) and severe oligozoospermia (n=28). The patients underwent clinical, andrological and laboratory-instrumental examination: ultrasound of the scrotum, spermatological, hormonal, cytogenetic, molecular cytogenetic (FISH) and molecular genetic examination of loci or genes associated with male fertility disorders (AZF, CFTR, AR). Results. Various genetic factors of male infertility were found in 99 (49.5%) of 200 patients, including 76 (45.7%) men with azoospermia and 23 (82.1%) patients with severe oligozoospermia. Cystic fibrosis and CBAVD syndrome were diagnosed in 4.5% of patients, congenital hypogonadotropic hypogonadism - in 7.5% of men. Karyotype abnormalities were found in 52 (26.8%) patients, including Klinefelter syndrome (47,XXY; n=34), disomy Y (47,XYY; n=6), 46,XX-testicular disorder of sex development (n=3), balanced autosomal abnormalities (n=9). According to the results of the FISH analysis, no cryptic mosaicism was found in patients with sex chromosomes aneuploidy. Pathogenic Y chromosome microdeletions in the AZF locus (Y q11.2) were found in 16 (8%) patients. Pathogenic variants of the CFTR gene were detected in 9 patients with cystic fibrosis and CBAVD syndrome. Conclusions. Comprehensive genetic examination can significantly improve the effectiveness of the diagnosis of genetically determined forms of male infertility associated with severe pathozoospermia. To identify rare non-syndromic genetic forms of male fertility associated with gene variants and copy number variations, it is necessary to use massive parallel sequencing, array comparative genomic hybridization and other genomic analysis methods.

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SANDERS, KATE L., ARNE R. RASMUSSEN, JOHAN ELMBERG, MUMPUNI _, MICHAEL GUINEA, PETER BLIAS, MICHAEL S. Y. LEE, and BRYAN G. FRY. "Aipysurus mosaicus, a new species of egg-eating sea snake (Elapidae: Hydrophiinae), with a redescription of Aipysurus eydouxii (Gray, 1849)." Zootaxa 3431, no. 1 (August 21, 2012): 1. http://dx.doi.org/10.11646/zootaxa.3431.1.1.

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We describe a new species of egg-eating sea snake, Aipysurus mosaicus sp. nov., from northern Australia and southernNew Guinea. This species was previously considered to be an allopatric population of A. eydouxii, which occursthroughout the Sunda Shelf and in New Guinea. Molecular analyses reveal these two species to be sister lineages withfixed nucleotide substitutions at three independent mitochondrial and nuclear loci, and a deep phylogenetic divergenceexceeding that of all other sampled species pairs in Aipysurus. Aipysurus mosaicus sp. nov. is also distinguished from A.eydouxii by morphological characters relating to scalation (e.g. number of ventral scales), colour pattern (e.g. number andshape of transverse body bands), internal soft anatomy (e.g. position of heart in relation to ventral scales), and skeletalmorphology (e.g. shape of nasal and caudal neural spines). Additional sampling is needed to clarify the extent ofgeographic contact between A. eydouxii and the new species in New Guinea where they appear to be sympatric. It is likelythat the boundaries between these taxa will be mirrored in other coastal sea snakes with ranges spanning the deep watersof the Timor Trench; discovery of such cryptic species will have important implications for conservation of this highly diverse but relatively poorly studied group of marine vertebrates.

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Schwartz, Jason R., Michael P. Walsh, Jing Ma, Tamara Lamprecht, Shuoguo Wang, Gang Wu, John Easton, Raul C. Ribeiro, and Jeffery M. Klco. "The Genomic Landscape of Pediatric Myelodysplastic Syndromes." Blood 128, no. 22 (December 2, 2016): 956. http://dx.doi.org/10.1182/blood.v128.22.956.956.

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Abstract Myelodysplastic syndromes are uncommon in children (incidence of ~2 cases/million) and have a poor prognosis. Despite the wealth of knowledge about the genomic landscape of adult MDS, much less is understood about pediatric MDS, and many recurrent mutations found in adults are not common in children (Hirabayashi, Blood 2012). Furthermore, the clinical presentation, bone marrow morphology, and cytogenetic abnormalities are also different when comparing adult and pediatric MDS, suggesting disparate underlying mechanisms. Here we describe the somatic and germline genomic landscape of pediatric MDS using whole exome sequencing (WES) and RNA-sequencing. We evaluated 88 diagnostic bone marrow samples obtained from the St. Jude Children's Research Hospital Tissue Bank from patients diagnosed between 1988 and 2015. This cohort contains 34 primary MDS, including Refractory Cytopenia of Childhood/RCC (n=19) and Refractory Anemia with Excess Blasts/RAEB (n=15). For comparison, we also included 32 treatment-related (tMDS), 14 MDS/MPN (including 10 Juvenile Myelomonocytic Leukemia/JMML), and 8 cases of AML with Myelodysplasia-Related Changes/AML-MRC (including 5 cases that previously would have been classified as RAEB in transformation/RAEB-T). WES was completed for 87 tumor/normal pairs (tumor only, n=1) using the Nextera Rapid Capture Expanded Exome (Illumina). Normal comparator gDNA was obtained from flow-sorted lymphocytes and variants were classified as germline if present at greater than 30% variant allele frequency (VAF) in the lymphocyte sample; thus, bone marrow mosaicism cannot be excluded. Mean sequencing coverage for the tumor and normal samples were 102x and 105x, respectively. An average of 7.9 variants were observed per patient in the primary MDS cohort (RCC=6.3, RAEB=10.2), compared to 25.5/patient in the tMDS cohort (p=0.001). Copy number information, obtained from WES data, determined that deletions involving chromosome 7 were frequent (n=28, 32%). Approximately 50% of RCC cases had deletions involving chromosome 7 (9 of 19), compared to only 20% of RAEB cases (3 of 15). Amplification of chromosomes 8 (n=7, 8%) and 21 (n=6, 7%), and deletions of 17 (n=5, 6%) were present at low frequency. In total, we detected 43 additional copy number abnormalities (including 9 cryptic chromosome 7 abnormalities) with WES compared to standard conventional karyotyping. RAS/MAPK pathway mutations were present in 42% of the patients (49 total mutations in 37 cases, including 4 germline variants). Fourteen of the 34 primary MDS cases (41%) had at least one RAS/MAPK mutation, including 13 somatic and 2 germline variants. Mutations in RNA splicing genes (germline, n=0; somatic, n=7; 8% of cohort) were less common, unlike what is observed in adult MDS. As expected, 2 patients with JMML harbored germline variants in PTPN11 and NF1. Surprisingly, presumed germline variants were detected in RRAS and NF1 in patients with primary MDS. Germline variants in transcription factors seen in familial MDS/AML (e.g., RUNX1, CEBPA, ETV6, GATA2) were uncommon, although a germline GATA2 variant was found in a single AML-MRC case. RNA-seq using the TruSeq (Illumina) Stranded RNA protocol was performed on 70 samples with suitable RNA. Fusion transcripts were uncommon in primary MDS, while fusions involving KMT2A, NUP98, RUNX1, MECOM, and ETV6were detected in the tMDS and AML-MRC cohorts. Although many of the mutations affecting the RAS/MAPK pathway were in common genes (NRAS, PTPN11, NF1, or CBL), many other mutations were in genes less frequently reported to be mutated in myeloid neoplasms, such as BRAF, SOS1, RIT1 and RRAS. We demonstrated that the mutations in BRAF (G469A, D594N, N581I) and SOS1 (E433K, G328R, S548R) found in our cohort activate the RAS/MAPK pathway to variable levels, as measured by ERK phosphorylation. In addition, expression of the BRAFvariants conferred IL3-independence in Ba/F3 cells. In conclusion, we show that the genomic landscapes of pediatric and adult MDS are different, namely in patterns of RAS/MAPK pathway and RNA splicing gene mutations, thus supporting the notion that MDS in adults and children comprise unique biological entities. The enrichment of RAS/MAPK mutations in pediatric MDS suggests biologic overlap with JMML and may provide direction for future therapeutic options. Disclosures No relevant conflicts of interest to declare.

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Dinsdale, A., N. A. Schellhorn, P. De Barro, Y. M. Buckley, and C. Riginos. "Rapid genetic turnover in populations of the insect pest Bemisia tabaci Middle East: Asia Minor 1 in an agricultural landscape." Bulletin of Entomological Research 102, no. 5 (March 15, 2012): 539–49. http://dx.doi.org/10.1017/s0007485312000077.

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AbstractOrganisms differ greatly in dispersal ability, and landscapes differ in amenability to an organism's movement. Thus, landscape structure and heterogeneity can affect genetic composition of populations. While many agricultural pests are known for their ability to disperse rapidly, it is unclear how fast and over what spatial scale insect pests might respond to the temporally dynamic agricultural landscapes they inhabit. We used population genetic analyses of a severe crop pest, a member of the Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidea) cryptic species complex known as Middle East-Asia Minor 1 (commonly known as biotype B), to estimate spatial and temporal genetic diversity over four months of the 2006–2007 summer growing season. We examined 559 individuals from eight sites, which were scored for eight microsatellite loci. Temporal genetic structure greatly exceeded spatial structure. There was significant temporal change in local genetic composition from the beginning to the end of the season accompanied by heterozygote deficits and inbreeding. This temporal structure suggests entire cohorts of pests can occupy a large and variable agricultural landscape but are rapidly replaced. These rapid genetic fluctuations reinforce the concept that agricultural landscapes are dynamic mosaics in time and space and may contribute to better decisions for pest and insecticide resistance management.

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Santos, Xavier, Vicenç Bros, and Elisabet Ros. "Contrasting responses of two xerophilous land snails to fire and natural reforestation." Contributions to Zoology 81, no. 3 (August 24, 2012): 167—S1. http://dx.doi.org/10.1163/18759866-08103004.

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Land-use change is considered the main disturbance in landscape structure and composition, directly affecting faunal distribution and species richness worldwide. Wildfires and natural reforestation alter habitat structure in terms of vegetation cover and also in soil composition and moisture; these processes hence trigger habitat transformations that act as opposing forces at small spatial scales. We have explored the contrasting effects of wildfires and natural reforestation on two land-snail species of the genus Xerocrassa, which are endemic in the western Mediterranean. Snails were sampled in pine and Holm oak forest, stony bare slopes and burnt sites. Both species followed a similar pattern: they were present in more than 75% of the stony bare slope sites and around 50% of the burnt sites, but were almost absent in Holm oak forests. The comparison of aerial photographs from 1956 and 2003 showed that stony bare slopes were significantly larger in 1956, this indicating that the natural reforestation might close these habitats, and consequently threaten the viability of the Xerocrassa populations. Given their limited mobility, the presence of Xerocrassa at burnt sites suggests that these species live in small and cryptic populations within the forest, surviving fire and expanding their distribution due to the appearance of adequate habitats. Our study shows that natural reforestation and fire play opposing roles in conserving Xerocrassa populations. The preservation of stony bare slopes as well as other open areas is a key management guideline to maintain landscape mosaics and help future conservation of species of open habitats such as these vulnerable endemic gastropods.

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Hook, Ernest B., and Dorothy Warburton. "Turner syndrome revisited: review of new data supports the hypothesis that all viable 45,X cases are cryptic mosaics with a rescue cell line, implying an origin by mitotic loss." Human Genetics 133, no. 4 (January 30, 2014): 417–24. http://dx.doi.org/10.1007/s00439-014-1420-x.

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Ma, Na, Hui Xi, Jing Chen, Ying Peng, Zhengjun Jia, Shuting Yang, Jiancheng Hu, et al. "Integrated CNV-seq, karyotyping and SNP-array analyses for effective prenatal diagnosis of chromosomal mosaicism." BMC Medical Genomics 14, no. 1 (February 25, 2021). http://dx.doi.org/10.1186/s12920-021-00899-x.

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Abstract Background Emerging studies suggest that low‐coverage massively parallel copy number variation sequencing (CNV-seq) more sensitive than chromosomal microarray analysis (CMA) for detecting low-level mosaicism. However, a retrospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. Methods A total of 72 mosaicism cases identified by karyotyping or CMA were recruited to the study. There were 67 mosaic samples co-analysed by CMA and CNV-seq, comprising 40 with sex chromosome aneuploidy, 22 with autosomal aneuploidy and 5 with large cryptic genomic rearrangements. Results Of the 67 positive mosaic cases, the levels of mosaicism defined by CNV-seq ranged from 6 to 92% compared to the ratio from 3 to 90% by karyotyping and 20% to 72% by CMA. CNV-seq not only identified all 43 chromosomal aneuploidies or large cryptic genomic rearrangements detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. The improved yield of mosaicism detection by CNV-seq was largely due to the ability to detect low level mosaicism below 20%. Conclusion In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant mosaicism with enhanced resolution and increased sensitivity. This study provides strong evidence for applying CNV-seq as an alternative to CMA for detection of aneuploidy and mosaic variants.

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Araújo, A., and E. S. Ramos. "Cryptic mosaicism involving a second chromosome X in patients with Turner syndrome." Brazilian Journal of Medical and Biological Research 41, no. 5 (May 2008). http://dx.doi.org/10.1590/s0100-879x2008000500004.

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Rubinstein, Clifford Dustin, Dalton T. McLean, Brent P. Lehman, Jennifer J. Meudt, Dominic T. Schomberg, Kathy J. Krentz, Jamie L. Reichert, et al. "Assessment of Mosaicism and Detection of Cryptic Alleles in CRISPR/Cas9-Engineered Neurofibromatosis Type 1 and TP53 Mutant Porcine Models Reveals Overlooked Challenges in Precision Modeling of Human Diseases." Frontiers in Genetics 12 (September 23, 2021). http://dx.doi.org/10.3389/fgene.2021.721045.

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Genome editing in pigs has been made efficient, practical, and economically viable by the CRISPR/Cas9 platform, representing a promising new era in translational modeling of human disease for research and preclinical development of therapies and devices. Porcine embryo microinjection provides a universally available, efficient option over somatic-cell nuclear transfer, but requires that critical considerations be made in genotypic validation of the models that routinely go unaddressed. Accurate validation of genotypes is especially important when modeling genetic disorders, such as neurofibromatosis type 1 (NF1) that exhibits complex genotype–phenotypic relationships. NF1, an autosomal dominant disorder, is particularly hard to model as it manifests very differently across patients, and even within families, with over 3,000 disease-associated mutations of the neurofibromin 1 (NF1) gene identified. The precise nature of the mutations plays a role in the complex phenotypic presentation of the disorder that includes benign and malignant peripheral and central nervous system tumors, a variety of motor deficits and debilitating cognitive impairments and musculoskeletal, cardiovascular, and gastrointestinal disorders. NF1 can also often involve mutations in passenger genes such as TP53. In this manuscript, we describe the creation of three novel porcine models of NF1 and a model additionally harboring a mutation in TP53 by embryo microinjection of CRISPR/Cas9. We present the challenges encountered in validation of genotypes and the methodological strategies developed to counter the hurdles. We present simple options for quantifying level of mosaicism: a quantitative method (targeted amplicon sequencing) for small edits such as SNPs and indels and a semiquantitative method (competitive PCR) for large edits. Characterization of mosaicism allowed for strategic selection of founder pigs for rapid, economical expansion of genetically defined lines. We also present commonly observed unexpected DNA repair products (i.e., structural variants or cryptic alleles) that are refractory to PCR amplification and thus evade detection. We present the use of copy number variance assays to overcome hurdles in detecting cryptic alleles. The report provides a framework for genotypic validation of porcine models created by embryo microinjection and the expansion of lines in an efficient manner.

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Nadesapillai, Sapthami, Janielle van der Velden, Dominique Smeets, Guillaume van de Zande, Didi Braat, Kathrin Fleischer, and Ronald Peek. "Why are some patients with 45,X Turner syndrome fertile? A young girl with classical 45,X Turner syndrome and a cryptic mosaicism in the ovary." Fertility and Sterility, December 2020. http://dx.doi.org/10.1016/j.fertnstert.2020.11.006.

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Liehr, Thomas. "Uniparental disomy is a chromosomic disorder in the first place." Molecular Cytogenetics 15, no. 1 (February 17, 2022). http://dx.doi.org/10.1186/s13039-022-00585-2.

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Abstract Background Uniparental disomy (UPD) is well-known to be closely intermingled with imprinting disorders. Besides, UPD can lead to a disease by ‘activation’ of a recessive gene mutation or due to incomplete (cryptic) trisomic rescue. Corresponding to all common theories how UPD forms, it takes place as a consequence of a “chromosomic problem”, like an aneuploidy or a chromosomal rearrangement. Nonetheless, UPD is rarely considered as a cytogenetic, but most often as a molecular genetic problem. Results Here a review on the ~ 4900 published UPD-cases is provided, and even though being biased as discussed in the paper, the following insights have been given from that analysis: (1) the rate of maternal to paternal UPD is 2~3 to 1; (2) at most only ~ 0.03% of the available UPD cases are grasped scientifically, yet; (3) frequencies of single whole-chromosome UPDs are non-random, with UPD(16) and UPD(15) being most frequent in clinically healthy and diseased people, respectively; (4) there is a direct correlation of UPD frequency and known frequent first trimester trisomies, except for chromosomes 1, 5, 11 and 18 (which can be explained); (5) heterodisomy is under- and UPD-mosaicism is over-represented in recent reports; and (6) cytogenetics is not considered enough when a UPD is identified. Conclusions As UPD is diagnosed using molecular genetic approaches, and thus by specialists considering chromosomes at best as a whim of nature, most UPD reports lack the chromosomal aspect. Here it is affirmed and substantiated by corresponding data that UPD is a chromosomic disorder in the first place and cytogenetic analyses is indicated in each diagnosed UPD-case.

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Journal articles on the topic 'Cryptic Mosaicism'

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