Clinical utility of periodic reinterpretation of CNVs of uncertain significance: an 8-year retrospective study.

BACKGROUND: Array-CGH is the first-tier genetic test both in pre- and postnatal developmental disorders worldwide. Variants of uncertain significance (VUS) represent around 10~15% of reported copy number variants (CNVs). Even though VUS reanalysis has become usual in practice, no long-term study regarding CNV reinterpretation has been reported. METHODS: This retrospective study examined 1641 CGH arrays performed over 8 years (2010-2017) to demonstrate the contribution of periodically re-analyzing CNVs of uncertain significance. CNVs were classified using AnnotSV on the one hand and manually curated on the other hand. The classification was based on the 2020 American College of Medical Genetics (ACMG) criteria. RESULTS: Of the 1641 array-CGH analyzed, 259 (15.7%) showed at least one CNV initially reported as of uncertain significance. After reinterpretation, 106 of the 259 patients (40.9%) changed categories, and 12 of 259 (4.6%) had a VUS reclassified to likely pathogenic or pathogenic. Six were predisposing factors for neurodevelopmental disorder/autism spectrum disorder (ASD). CNV type (gain or loss) does not seem to impact the reclassification rate, unlike the length of the CNV: 75% of CNVs downgraded to benign or likely benign are less than 500 kb in size. CONCLUSIONS: This study's high rate of reinterpretation suggests that CNV interpretation has rapidly evolved since 2010, thanks to the continuous enrichment of available databases. The reinterpreted CNV explained the phenotype for ten patients, leading to optimal genetic counseling. These findings suggest that CNVs should be reinterpreted at least every 2 years.

Putative founder effect of Arg338* AP4M1 (SPG50) variant causing severe intellectual disability, epilepsy and spastic paraplegia: Report of three families.

Bi-allelic variants affecting one of the four genes encoding the AP4 subunits are responsible for the "AP4 deficiency syndrome." Core features include hypotonia that progresses to hypertonia and spastic paraplegia, intellectual disability, postnatal microcephaly, epilepsy, and neuroimaging features. Namely, AP4M1 (SPG50) is involved in autosomal recessive spastic paraplegia 50 (MIM#612936). We report on three patients with core features from three unrelated consanguineous families originating from the Middle East. Exome sequencing identified the same homozygous nonsense variant: NM_004722.4(AP4M1):c.1012C>T p.Arg338* (rs146262009). So far, four patients from three other families carrying this homozygous variant have been reported worldwide. We describe their phenotype and compare it to the phenotype of patients with other variants in AP4M1. We construct a shared single-nucleotide polymorphism (SNP) haplotype around AP4M1 in four families and suggest a probable founder effect of Arg338* AP4M1 variant with a common ancestor most likely of Turkish origin.

Mosaic complete tetrasomy 21 in a fetus with complete atrioventricular septal defect and minor morphological variations.

BACKGROUND: Tetrasomy 21 is a very rare aneuploidy which could clinically resemble a Down syndrome. It was most often described in its partial form than complete. We report the prenatal, pathological and genetic characteristics of a fetus with mosaic complete tetrasomy 21. This is the second well-documented description of a complete tetrasomy 21 in the literature. METHODS: Prenatal and fetal pathological examinations, cytogenetic and molecular analyses were performed to characterize fetal features with tetrasomy 21. RESULTS: Prenatal ultrasound examination revealed an isolated complete atrioventricular septal defect with normal karyotype on amniotic fluid. After termination of pregnancy, clinical examination of the fetus evoked trisomy 21 or Down syndrome. Chromosomal microarray analysis and FISH on lung tissue showed a mosaicism with four copies of chromosome 21 (tetrasomy 21). CONCLUSION: Our observation and the review of the literature reported the possibility of very weak mosaicism and disease-causing confined tissue-specific mosaicism in fetus or alive patients with chromosome 21 aneuploidy, mainly Down syndrome. In case of clinical diagnosis suggestive of Down syndrome, attention must be paid to the risk of false-negative test due to chromosomal mosaicism (very weak percentage, different tissue distribution). To overcome this risk, it is necessary to privilege the diagnostic techniques without culture step and to increase the number of cells and tissues analyzed, if possible. This study highlights the limits of microarray as the unique diagnostic approach in case of weak mosaic and French cytogenetics guidelines recommend to check anomalies seen in microarray by another technique on the same tissue.

Chromothripsis: potential origin in gametogenesis and preimplantation cell divisions. A review.

OBJECTIVE: To review the discovery of chromothripsis and analyze its impact on human reproduction. DESIGN: Database and literature analysis. SETTING: University hospital. PATIENT(S): Carriers of massive and complex chromosomal rearrangements. INTERVENTION(S): Cytogenetic analysis and molecular testing (fluorescence in situ hybridization, microarray, whole-genome sequencing). MAIN OUTCOME MEASURE(S): Chromothripsis occurrence in human gametes and preimplantation embryos, with regard to the potential causative mechanisms described in literature. RESULT(S): Databases were searched for the literature published up to March 2014. Chromothripsis is characterized by the shattering of one (or a few) chromosome segments followed by a haphazard reassembly of the fragments generated, arising through a single initial catastrophic event. Several mechanisms involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and the genesis of chromosomal abnormalities. Specific features of gametogenesis and early embryonic development such as the weakness of cell cycle and mitosis checkpoints and the rapid kinetics of division in germ cells and early cleavage embryos may contribute to the emergence of chromothripsis. CONCLUSION(S): The discovery of this new class of massive chromosomal rearrangement has deeply modified our understanding on the genesis of complex genomic rearrangements. Data presented in this review support the assumption that chromothripsis could operate in human germlines and during early embryonic development. Chromothripsis might arise more frequently than previously thought in both gametogenesis and early human embryogenesis.

[Chromothripsis, an unexpected novel form of complexity for chromosomal rearrangements]. / Le chromothripsis - Une forme insoupçonnée de complexification extrême des remaniements chromosomiques.

The recent discovery of a new kind of massive chromosomal rearrangement in different cancers, named "chromothripsis" (chromo for chromosome, thripsis for shattering) has questioned the established models for a progressive development of tumors. Indeed, this phenomenon, which is characterized by the shattering of one (or a few) chromosome segments followed by a random reassembly of the fragments generated, occurs during one unique cellular event. The same phenomenon was identified in constitutional genetics in patients with various developmental pathologies, indicating that chromothripsis also occurs at the germ cell level. Diverse situations can cause chromothripsis (radiations, telomere erosion, abortive apoptosis, etc.), and two express "repair routes" are used by the cell to chaotically reorganise the chromosomal regions concerned: non-homologous end-joining and repair by replicative stress. The in-depth analysis of the DNA sequences involved in the regions of chromothripsis leads to a better understanding of the molecular basis of chromothripsis and also helps to better apprehend its unexpected role in the development of constitutional pathologies and the progression of cancers.

[Complex chromosomal rearrangements: a paradigm for the study of chromosomal instability]. / Les remaniements chromosomiques complexes - un paradigme pour l'étude de l'instabilité chromosomique.

Complex chromosomal rearrangements (CCR) include diverse structural anomalies leading to complex karyotypes which are difficult to interpret. Although karyotype analysis has been able to identify a large number of these rearrangements and to distinguish de novo and familial events, it is the advent of molecular cytogenetic and sequence analysis techniques which have led to an understanding of the molecular mechanisms underlying the formation of CCR. The diversity and high level of complexity inherent to CCR raises questions about their origin, their ties to chromosome instability and their impact in pathology. Today it is possible to precisely characterize CCR and to offer carriers sophisticated diagnostic techniques, such as preimplantation diagnosis. However, the meiotic segregation of these rearrangements remains very complex.

Somatic mosaicism in trichorhinophalangeal syndrome: a lesson for genetic counseling.

Trichorhinophalangeal syndrome type I (TRPSI) is a genetic disorder characterized by sparse hair, a bulbous nasal tip, short stature with severe generalized shortening of all phalanges, metacarpal and metatarsal bones and cone-shaped epiphyses. This syndrome is caused by autosomal dominant mutations in the TRPS1 gene. However, because recurrence has been observed in siblings from healthy parents, an autosomal recessive mode of inheritance has also been suggested. We report on a male patient, born to healthy unrelated parents, with TRPSI. Using Sanger sequencing, we identified a mutation in the TRPS1 gene (c.2735 G>A, P.Cys912Tyr). The same mutation was detected as a 10% mosaic mutation by Pyrosequencing in blood-derived DNA from his healthy mother. To our knowledge, this is the first time that somatic mosaicism has been identified in TRPSI. This data combined with the observations of recurrences in siblings from healthy parents modifies the genetic counseling for TRPSI, which should discuss a 5-10 percent recurrence risk for healthy parents with an affected child because of the possibility of germinal mosaicism.

Expanding the phenotype of IQSEC2 mutations: truncating mutations in severe intellectual disability.

Intellectual disability (ID) is frequent in the general population, with 1 in 50 individuals directly affected worldwide. The multiple etiologies include X-linked ID (XLID). Among syndromic XLID, few syndromes present severe ID associated with postnatal microcephaly and midline stereotypic hand movements. We report on three male patients with ID, midline stereotypic hand movements, hypotonia, hyperkinesia, strabismus, as well as seizures (2/3), and non-inherited and postnatal onset microcephaly (2/3). Using array CGH and exome sequencing we characterised two truncating mutations in IQSEC2, namely two de novo intragenic duplication mapped to the Xp11.22 region and a nonsense mutation in exon 7. We propose that truncating mutations in IQSEC2 are responsible for syndromic severe ID in male patients and should be screened in patients without mutations in MECP2, FOXG1, CDKL5 and MEF2C.

CEP57 mutation in a girl with mosaic variegated aneuploidy syndrome.

Mosaic variegated aneuploidy (MVA) is a rare autosomal recessive disorder characterized by constitutional aneuploidies. Mutations in BUB1B and CEP57 genes, which are involved in mitotic spindle and microtubule stabilization, respectively, are responsible for a subset of patients with MVA. To date, CEP57 mutations have been reported only in four probands. We report on a girl with this disorder due to c.915-925dup11 mutation in CEP57, which predicts p.Leu309ProfsX9 and review the literature in order to facilitate genotype-phenotype correlation. Rhizomelic shortening of the upper limbs, skull anomalies with conserved head circumference, and absence of tumor development could be features suggesting a need for molecular screening of the CEP57 gene in patients with this disorder.

Early-onset obesity and paternal 2pter deletion encompassing the ACP1, TMEM18, and MYT1L genes.

Obesity is a common but highly, clinically, and genetically heterogeneous disease. Deletion of the terminal region of the short arm of chromosome 2 is rare and has been reported in about 13 patients in the literature often associated with a Prader-Willi-like phenotype. We report on five unrelated patients with 2p25 deletion of paternal origin presenting with early-onset obesity, hyperphagia, intellectual deficiency, and behavioural difficulties. Among these patients, three had de novo pure 2pter deletions, one presented with a paternal derivative der(2)t(2;15)(p25.3;q26) with deletion in the 2pter region and the last patient presented with an interstitial 2p25 deletion. The size of the deletions was characterized by SNP array or array-CGH and was confirmed by fluorescence in situ hybridization (FISH) studies. Four patients shared a 2p25.3 deletion with a minimal critical region estimated at 1.97 Mb and encompassing seven genes, namely SH3HYL1, ACP1, TMEMI8, SNTG2, TPO, PXDN, and MYT1L genes. The fifth patient had a smaller interstitial deletion encompassing the TPO, PXDN, and MYT1L genes. Paternal origin of the deletion was determined by genotyping using microsatellite markers. Analysis of the genes encompassed in the deleted region led us to speculate that the ACP1, TMEM18, and/or MYT1L genes might be involved in early-onset obesity. In addition, intellectual deficiency and behavioural troubles can be explained by the heterozygous loss of the SNTG2 and MYT1L genes. Finally, we discuss the parent-of-origin of the deletion.

Dysspondyloenchondromatosis without COL2A1 mutation: possible genetic heterogeneity.

Dysspondyloenchondromatosis is a rare form of generalized enchondromatosis associated with spinal involvement. This skeletal dysplasia is characterized by multiple enchondromas present in vertebrae as well as in metaphyseal and diaphyseal parts of the long tubular bones, post-natal short stature, and early development of kyphoscoliosis. A novel heterozygous missense mutation in COL2A1 was recently identified in a patient with dysspondyloenchondromatosis. This suggests that dysspondyloenchondromatosis might expand the already broad spectrum of type II collagenopathies. Here, we report on a young girl with features of dysspondyloenchondromatosis, specifically short stature, thoracoscoliosis, and generalized enchondromas lesions. Sanger sequencing failed to detect a mutation in COL2A1. We therefore suggest that dysspondyloenchondromatosis is a genetically heterogeneous condition.

Duplication 8q12: confirmation of a novel recognizable phenotype with duane retraction syndrome and developmental delay.

Duane retraction syndrome (DRS) is a rare congenital strabismus condition with genetic heterogeneity. DRS associated with intellectual disability or developmental delay is observed in several genetic diseases: syndromes such as Goldenhar or Wildervanck syndrome and chromosomal anomalies such as 12q12 deletion. We report on the case of a patient with DRS, developmental delay and particular facial features (horizontal and flared eyebrows, long and smooth philtrum, thin upper lip, full lower lip and full cheeks). We identified a duplication of the long arm of chromosome 8 (8q12) with SNP-array. This is the third case of a patient with common clinical features and 8q12 duplication described in the literature. The minimal critical region is 1.2 Mb and encompasses four genes: CA8, RAB2, RLBP1L1 and CHD7. To our knowledge, no information is available in the literature regarding pathological effects caused by to overexpression of these genes. However, loss of function of the CHD7 gene leads to CHARGE syndrome, suggesting a possible role of the overexpression of this gene in the phenotype observed in 8q12 duplication patients. We have observed that patients with 8q12 duplication share a common recognizable phenotype characterized by DRS, developmental delay and facial features. Such data combined to the literature strongly suggest that this entity may define a novel syndrome. We hypothesize that CHD7 duplication is responsible for a part of the features observed in 8q12.2 duplication.

Meiotic segregation of complex reciprocal translocations: direct analysis of the spermatozoa of a t(5;13;14) carrier.

OBJECTIVE: To directly study the meiotic segregation of a complex reciprocal translocation (CCR) as well as the occurrence of an interchromosomal effect. DESIGN: In situ sperm fluorescence in situ hybridization (FISH) analysis. SETTING: Department of Cytogenetics and INSERM research center. PATIENT(S): A male carrier of a balanced complex reciprocal translocation t(5;13;14)(q23;q21;q31). INTERVENTION(S): Sperm samples from the carrier and direct FISH analysis on sperm slide preparations. MAIN OUTCOME MEASURE(S): Meiotic segregation pattern determined on sperm nuclei and estimation of the incidence of unbalanced spermatozoa and an interchromosomal effect (ICE). RESULT(S): Only 27% of spermatozoa displayed a normal or balanced chromosome complement. The rate of unbalanced sperm was 69.4%, including different types of 3:3, 4:2, and 5:1 segregations. There was no evidence for the occurrence of an interchromosomal effect in autosomal chromosomes, but the gonosomes displayed a statistically significant increase in disomy rates. CONCLUSION(S): These results are consistent with the formation of a hexavalent configuration at the pachytene stage of meiosis and a high prevalence of imbalance production. The mechanisms of formation of CCRs must be examined with regard to these direct results and new molecular data on the formation of genomic rearrangements.

Breakpoint mapping and complete analysis of meiotic segregation patterns in three men heterozygous for paracentric inversions.

Paracentric inversions (PAIs) are structural chromosomal rearrangements generally considered to be harmless. To date, only a few studies have been performed concerning the meiotic segregation of these rearrangements, using either the human-hamster fertilization system or fluorescence in situ hybridization (FISH) with centromeric or telomeric DNA probes. To improve the assessment of imbalances in PAI, we present a new strategy based on FISH assay using multiple bacterial artificial chromosome probes, which allow a precise localization of chromosome break points and the identification of all meiotic products in human sperm. Sperm samples of three cases with PAI were investigated: an inv(5)(q13.2q33.1), an inv(9)(q21.2q34.13) and an inv(14)(q23.2q32.13). The frequencies of spermatozoa with inverted chromosomes were 44.7% in inv(5), 42.7% in inv(9) and 46.7% in inv(14). The global incidences of unbalanced complements were 9.7, 12.6 and 3.7% in inv(5), inv(9) and inv(14), respectively. This report is the first study providing a detailed description of meiotic segregation patterns in human sperm by using a sperm FISH approach. This study demonstrates that the detailed analysis of segregation in PAI may provide important data for both genetic analysis and counseling of inversion carriers.

Prader-Willi syndrome: is there a recognizable fetal phenotype?

OBJECTIVES: To determine fetal features, which could lead to the diagnosis of Prader-Willi syndrome (PWS) during pregnancy. METHODS: We analyze the ultrasound features, genetic studies and pathologic findings in two cases of PWS diagnosed during pregnancy. RESULTS: In the first case, diminished fetal movement, polyhydramnios and oddly positioned hands and feet suggested PWS. Methylation studies confirmed diagnosis and a deletion was detected in the 15q11-q13 region. In the second case, similar ultrasound findings led to prenatal diagnosis of PWS with an abnormal methylation pattern compatible with uniparental disomy. Both fetuses had a characteristic appearance at 28 and 30 weeks' gestation, which included a peculiar position of hands with flexed wrists and dorsi-extended feet with flexed toes. CONCLUSIONS: The peculiar position of the extremities combined with diminished fetal movement and polyhydramnios seems to be characteristic and should suggest PWS.

Mosaic trisomy 16 in a fetus: the complex relationship between phenotype and genetic mechanisms.

OBJECTIVES: This study was undertaken to discuss the workup of trisomy 16 pregnancies. STUDY DESIGN: This case study reports the prenatal detection and postnatal confirmation of mosaic trisomy 16, associated with uniparental disomy (UPD) 16, in a 34-year-old woman who showed elevated maternal serum alpha-fetoprotein and beta-HCG at a gestational age (GA) of 15.5 weeks. RESULTS: Amniotic fluid (AF) karyotyping at different GAs revealed various levels of trisomy 16 mosaicism (0 to level III). UPD studies at 21 weeks of gestation revealed maternal heterodisomy 16. Serial fetal ultrasonography showed fetal abnormalities: intrauterine growth restriction (IUGR), dilated digestive tract, and gallbladder agenesis. Postmortem examination confirmed the prenatal findings and revealed additional anomalies, such as hypoplastic cerebellum with abnormal gyration of the vermis. CONCLUSIONS: Workup following prenatal detection of trisomy 16 mosaicism in chorionic villi must include AF karyotyping and serial ultrasound examination of the fetus in order to approach postnatal developmental prognosis.

Analysis of sperm aneuploidy by PRINS.

Based on the direct in situ mixing of the colors of different fluorochromes (fluorescein isothiocyanate, tetramethylrhodamine isothiocyanate, Cascade Blue) incorporated in sequential primed in situ labeling (PRINS) reactions, a new multicolor PRINS procedure is described, allowing the rapid and distinct in situ labeling of three or four human chromosomes. Each PRINS reaction consists of a unique 5-min step for annealing and elongation. In combination with the 0.5 M NaOH pretreatment for simultaneous in situ denaturation and decondensation of sperm nuclei, this technique has been adapted to human sperm nuclei for the direct assessment of aneuploidy.

Partial epilepsy and 47,XXX karyotype: report of four cases.

Epilepsy is a common finding in chromosomal imbalances, but only a few chromosome abnormalities have a characteristic electro-clinical pattern. Trisomy X is one of the most common sex chromosome abnormalities in females, and is associated with considerable phenotypic variability. This report describes four 47,XXX females with mental deficiency and epilepsy. Although a specific electro-clinical pattern could not be defined, the epileptic phenotypes of these patients share many features; we suggest that the association 47,XXX/epilepsy/mental retardation may not be coincidental. This report also enlarges the clinical spectrum of the 47,XXX phenotype. Moreover, these observations highlight the critical role of chromosome X in epilepsy and mental retardation.