Optical Genome Mapping Reveals Disruption of the RASGRF2 Gene in a Patient with Developmental Delay Carrying a De Novo Balanced Reciprocal Translocation.

While balanced reciprocal translocations are relatively common, they often remain clinically silent unless they lead to the disruption of functional genes. In this study, we present the case of a boy exhibiting developmental delay and mild intellectual disability. Initial karyotyping revealed a translocation t(5;6)(q13;q23) between chromosomes 5 and 6 with limited resolution. Optical genome mapping (OGM) enabled a more precise depiction of the breakpoint regions involved in the reciprocal translocation. While the breakpoint region on chromosome 6 did not encompass any known gene, OGM revealed the disruption of the RASGRF2 (Ras protein-specific guanine nucleotide releasing factor 2) gene on chromosome 5, implicating RASGRF2 as a potential candidate gene contributing to the observed developmental delay in the patient. Variations in RASGRF2 have so far not been reported in developmental delay, but research on the RASGRF2 gene underscores its significance in various aspects of neurodevelopment, including synaptic plasticity, signaling pathways, and behavioral responses. This study highlights the utility of OGM in identifying breakpoint regions, providing possible insights into the understanding of neurodevelopmental disorders. It also helps affected individuals in gaining more knowledge about potential causes of their conditions.

New euchromatic variant dup(11)(p15.3p15.1) transmitted through two generations defined by low coverage whole genome sequencing.

We report on a 14-year old boy, his father, and his paternal uncle, all three carriers of a duplication of chromosomal region 11p15.3-p15.1. The aberration was transmitted by the grandmother, who is carrier of a balanced insertion 46,XX,ins(14;11)(q32.1;p15.3p15.1). In order to determine the precise molecular basis of this structural variant, we performed low-coverage whole genome sequencing on the boy's father. This approach allowed precise determination of the genomic breakpoints and revealed a duplication of 6.9 Mb, centromeric to the Beckwith-Wiedemann/Silver-Russell syndrome critical region in 11p15.5, that inserted in inverse orientation into 14q32.12 (according to HGVS nomenclature: NC_000014.8:g.92871000_92871001ins[NC_000011.9:g.12250642_19165928inv;T]). To our knowledge, this is the first report of a duplication of 11p15.3-p15.1 involving more than 40 genes and transmitted through two generations without apparent clinical effects.

Pre- and postnatal findings in a patient with a recombinant chromosome rec(8)(qter→q21.11::p23.3→qter) due to a paternal pericentric inversion inv(8)(p23.3q21.11) and review of the literature.

Recombinant chromosome 8 (Rec8) syndrome (San Luis Valley [SLV] syndrome; OMIM #179613) is a rare chromosome disorder associated with intellectual disability, congenital heart defects, variable skeletal and urogenital anomalies, and dysmorphic features. It is characterized by a partial terminal deletion of 8p and a partial terminal duplication of 8q, which is usually due to meiotic recombination of a pericentric inversion of chromosome 8 of a healthy carrier parent. There are only few reports of cases with breakpoints defined at the molecular level by molecular karyotyping. We report on a case of Rec8 syndrome with previously unreported breakpoints in a male fetus with intrauterine growth restriction, hypogenesis of the corpus callosum, bilateral cleft lip/palate, and congenital heart defect. Cytogenetic analysis revealed a recombinant chromosome 8 [46,XY,rec(8)(qter→q21.11::p23.3→qter)] secondary to a paternal pericentric inversion [46,XY,inv(8)(p23.3q21.11)]. Molecular karyotyping correspondingly showed a terminal copy number loss of 1.4 Mb (arr[hg19] 8p23.3(158048_1514749)×1) and a terminal copy number gain of chromosome band 8q21.11q24.3 of 69.8 Mb (arr[hg19] 8q21.11q24.3(76477367_146295771)×3). To our knowledge, this is the fourth reported case diagnosed prenatally. We describe the postnatal clinical course of the male newborn. Furthermore, we review and compare the phenotypic features and breakpoints of 74 reported Rec8/SLV cases.

Parental origin of deletions and duplications - about the necessity to check for cryptic inversions.

BACKGROUND: Copy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents. RESULTS: Seventy-four patients with different MMSs and overall 81 CNVs were studied here by a novel three color FISH approach. The way how three locus-specific probes are selected (one is the CRP and two are flanking it in a distance of 5-10 Mb) enables to detect or exclude two possible parental conditions as origins of the CNV seen in the index: (i) direct parental origin of the CNV (deletion or duplication) or (ii) a parental cryptic inversion. Thus, for overall 51/81 CNVs (63%) a parental origin could be determined. 36/51 (70.5%) inherited the CNV directly from one of the parents, but 15/51 (29.5%) were due to an exclusively by three color FISH detectable parental inversion. A 2:1 ratio of maternal versus paternal inheritance was found. Also almost two times more male than female were among the index patients. CONCLUSION: The new, here suggested three color FISH approach is suited for more comprehensive parental studies of patients with MMS. The detection rate for parental origin was increased by 140% in this study. Still, for 30/81 cases (37%) no reason for the 'de novo' MMS in the affected index patient could be found by the here suggested FISH-probe set.

Discordance between ultrasound and cell free DNA screening for monosomy X.

OBJECTIVE: Cell free DNA (cfDNA) testing has evolved as an important tool in prenatal screening for trisomy 21. It can also be used in screening for monosomy X. We perform a systemic review to determine the detection and false positive in screening for monosomy X and demonstrate a case that offers two possible explanations for the lower screening performance compared to trisomy 21. CASE: A 31-year-old primigravida was referred to us due to an abnormal cfDNA test indicating monosomy X. However, the genitalia was male. An amniocentesis was done that indicated 46,X,idic(Y)(q11.21). SNP array analysis confirmed the Ypter-q11.21 duplication. A phenotypically normal male baby was born at 40 weeks. Postnatal karyotyping of several pregnancy tissues was carried out. While in most samples the karyotype was 46,X,idic(Y)(q11.21), in the four placenta samples and in the amniotic membranes there was mosaicism of 46,X,idic(Y)(q11.21) and 45,X. DATA SOURCES: A search of the Medline and Embase database was done for articles about screening for monosomy X by cfDNA. We performed a systematic review to assess the detection and false-positive rate. RESULTS: Seven studies fulfilled the inclusion criteria. In summary, there were 153 pregnancies with monosomy X and 4116 euploid ones. The detection and false-positive rate was 94.1 and 0.53 %. CONCLUSION: Although the performance of cfDNA in prenatal screening for monosomy X is better than any other screening test, it is not comparable with invasive testing. One should be aware of the limitations especially if the ultrasound examination is contradictory with the cfDNA results.

Interstitial duplication of chromosome region 1q25.1q25.3: report of a patient with mild cognitive deficits, tall stature and facial dysmorphisms.

Isolated interstitial duplications of chromosome band 1q25 are apparently very rare; no patients with detailed molecular and clinical characterization of duplications restricted to this region have been published to date. We report on a 9-year-old girl with mild cognitive deficits, tall stature, macrocephaly and discrete dysmorphic features in whom a de novo interstitial 7.5 Mb duplication of 1q25.1q25.3 was detected by SNP array analysis (arr[hg19] 1q25.1q25.3(173,925,505-181,381,242)x3 dn). The duplicated region was inversely inserted into chromosome band 1q42.2: 46,XX,der(1)(pter→q42.2::q25.3→q25.1::q42.2→qter). Overexpression of one or several of the 87 genes in the duplicated interval was presumably the major causative factor for the clinical manifestations. Reports of additional patients with overlapping duplications will be needed to establish detailed karyotype-phenotype correlations and to gain a better understanding of the underlying pathomechanisms.

12q24.33 deletion: report of a patient with intellectual disability and review of the literature.

Deletions of chromosome band 12q24.33 are rare. We report on a 17-year-old male patient with intellectual disability but no major malformations or dysmorphic features in whom a de novo interstitial 660 kb deletion in 12q24.33 was detected by SNP array analysis. This deletion was secondary to a translocation t(12;14)(q24.3;q13)dn that also led to a small deletion in 14q21.1 and a small duplication in 2p23.1. The deletion overlaps with two previously published larger deletions in patients who suffered from intellectual disability, obesity, and polycystic kidney disease, indicating that haploinsufficiency of one or several of the genes in the deleted interval of the patient reported here causes intellectual deficits, but not obesity or renal problems. The 14 RefSeq genes that are harbored by this deletion include P2RX2, which had previously been proposed as a candidate gene for intellectual disability. Thus, the patient reported here broadens our knowledge of the phenotypic consequences of deletions in 12q24.33 and facilitates genotype-phenotype correlations for chromosome aberrations of this region.

De novo exceptional complex chromosomal rearrangement in a healthy fertile male: case report and review of the literature.

OBJECTIVE: To report a de novo exceptional complex chromosomal rearrangement (CCR) with four breakpoints in the male partner of a couple with recurrent abortions. DESIGN: Case report and review of the literature. SETTING: Genetics laboratory in a private hospital. PATIENT(S): A couple referred for recurrent abortions. INTERVENTION(S): Cytogenetic and sperm fluorescence in situ hybridization (FISH) techniques. MAIN OUTCOME MEASURE(S): Karyotype and FISH sperm results. RESULT(S): The couple was phenotypically normal, with no family history of miscarriage or infertility. Female karyotype was normal. Male karyotype followed by FISH analysis showed a de novo CCR with four breakpoints: t(5,13,16)(q11.1, q14.3, q12.2), ins(16;13)(q12.2;q?q14.2). ish t(5;13;16)(wcp5+,wcp13+), ins(16;13)(wcp13+). CONCLUSION(S): Exceptional de novo CCR male carriers with recurrent abortions are extremely rare. Patients with CCRs have limited options to achieve a normal pregnancy. Careful consideration and assessment should be provided upon counseling of couples with CCRs.

Chromosome 11p15 duplication in Silver-Russell syndrome due to a maternally inherited translocation t(11;15).

The role of 11p15 disturbances in the aetiology of Silver-Russell syndrome (SRS) is well established: in addition to hypomethylation of the H19/IGF2 differentially methylated regions, five patients with a duplication of maternal 11p15 material have been described. We report on a boy with SRS carrying a maternally inherited duplication of chromosome 11p15. The patient showed the typical clinical picture of SRS including severe intrauterine and postnatal growth restriction, relative macrocephaly, a prominent forehead, a triangular face, down-turned corners of the mouth and fifth digit clinodactyly. Body asymmetry was not observed. By molecular genetic analyses, MLPA and microsatellite typing detected a duplication of chromosome 11p15 and cytogenetic analysis showed an unbalanced translocation t(11;15)(p15.5:p12). The size of the duplicated region is approximately 8.8 Mb as determined by SNP-array analysis. The healthy mother carried a balanced reciprocal chromosome translocation t(11;15). Thus, there is an increased risk for further children with SRS due to 11p15 duplication. Additionally, the family is at risk for offspring with an 11p15 deletion and Beckwith-Wiedemann syndrome whereby the phenotype will be influenced by haploinsufficiency of additional genes at 11p15 due to the deletion. The balanced aberrant karyotype was identified in several other family members, but interestingly there was no history of recurrent miscarriages, intrauterine fetal death, or multiple congenital anomaly syndromes in the family.

Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study.

Genomic microarrays have been implemented in the diagnosis of patients with unexplained mental retardation. This method, although revolutionizing cytogenetics, is still limited to the detection of rare de novo copy number variants (CNVs). Genome-wide single nucleotide polymorphism (SNP) microarrays provide high-resolution genotype as well as CNV information in a single experiment. We hypothesize that the widespread use of these microarray platforms can be exploited to greatly improve our understanding of the genetic causes of mental retardation and many other common disorders, while already providing a robust platform for routine diagnostics. Here we report a detailed validation of Affymetrix 500k SNP microarrays for the detection of CNVs associated to mental retardation. After this validation we applied the same platform in a multicenter study to test a total of 120 patients with unexplained mental retardation and their parents. Rare de novo CNVs were identified in 15% of cases, showing the importance of this approach in daily clinical practice. In addition, much more genomic variation was observed in these patients as well as their parents. We provide all of these data for the scientific community to jointly enhance our understanding of these genomic variants and their potential role in this common disorder.

Small supernumerary marker chromosomes (SMCs): genotype-phenotype correlation and classification.

Small supernumerary marker chromosomes (SMCs) are present in about 0.05% of the human population. In approximately 30% of SMC carriers (excluding the approximately 60% SMC derived from one of the acrocentric chromosomes), an abnormal phenotype is observed. The clinical outcome of an SMC is difficult to predict as they can have different phenotypic consequences because of (1). differences in euchromatic DNA-content, (2). different degrees of mosaicism, and/or (3). uniparental disomy (UPD) of the chromosomes homologous to the SMC. Here, we present 35 SMCs, which are derived from all human chromosomes, apart from chromosome 6, as demonstrated by the appropriate molecular cytogenetic approaches, such as centromere-specific multicolor fluoresence in situ hybridization (cenM-FISH), multicolor banding (MCB), and subcentromere-specific multicolor FISH (subcenM-FISH). In nine cases without an aberrant phenotype, neither partial proximal trisomies nor UPD could be detected. Abnormal clinical findings, such as psychomotoric retardation and/or craniofacial dysmorphisms, were associated with seven of the cases in which subcentromeric single-copy probes were proven to be present in three copies. Conversely, in eight cases with a normal phenotype, proximal euchromatic material was detected as partial trisomy. UPD was studied in 12 cases and subsequently detected in two of the cases with SMC (partial UPD 4p and maternal UPD 22 in a der(22)-syndrome patient), indicating that SMC carriers have an enhanced risk for UPD. At present, small proximal trisomies of 1p, 1q, 2p, 6p, 6q, 7q, 9p, and 12q seem to lead to clinical manifestations, whereas partial proximal trisomies of 2q, 3p, 3q, 5q, 7p, 8p, 17p, and 18p may not be associated with significant clinical symptoms. With respect to clinical outcome, a classification of SMCs is proposed that considers molecular genetic and molecular cytogenetic characteristics as demonstrated by presently available methods.