Prader Willi/Angelman and DiGeorge/velocardiofacial syndrome deletions: Diagnosis by primed in situ labeling (PRINS)

A recently developed methodology—primed in situ labeling (PRINS)—can be used in place of fluorescence in situ hybridization (FISH) to diagnose microdeletions. To demonstrate the efficiency, sensitivity, and specificity of PRINS in the diagnosis of microdeletions, we studied groups of patients with Prader Willi/Angelman (PWS/AS) syndrome and DiGeorge/velocardiofacial syndrome (DGS/VCFS). Results obtained by PRINS were then confirmed with the results obtained with FISH. Oligonucleotide primers specific for SNRPN and GABRB3 were used for PWS/AS syndromes. For DGS/VCFS, the primers used were DGCR2/TUPLE1 loci. Labeling patterns obtained by PRINS and FISH were analyzed and scored under a fluorescence microscope. Five normal subjects served as controls and were used for standardization of the PRINS protocol. In all, 20 study patients were involved: 10 PWS/AS and 10 DGS/VCFS. Five of the 10 patients referred with the clinical diagnosis of PWS/AS showed absence of labeling for SNRPN and GABRB3 on one chromosome 15, confirming deletion of the two loci. Similarly, 6 of the 10 patients referred for DGS/VCFS showed deletion for the DGCR2/TUPLE1 loci on one chromosome 22. The remaining patients and controls had normal patterns for all the loci as indicated by FISH and PRINS. Concordant FISH and PRINS results were obtained in all patients and controls studied. © 2001 Wiley‐Liss, Inc.     

Origin of uniparental disomy 15 in patients with Prader‐Willi or Angelman syndrome

Maternal uniparental disomy (UPD) accounts for ∼25% of Prader‐Willi patients (PWS) and paternal UPD for about 2–5% of Angelman syndrome (AS) patients. These findings and the parental origin of deletions are evidence of genomic imprinting in the cause of PWS and AS. The natural occurrence of UPD individuals allows the study of meiotic mechanisms resulting in chromosomal nondisjunction (ND). We selected patients with UPD15 from our sample of 30 PWS and 40 AS patients to study the origin of ND and the recombination along chromosome 15. These patients were analyzed with 10 microsatellites throughout the entire chromosome 15 (D15S541, D15S542, D15S11, D15S113, GABRB3, CYP19, D15S117, D15S131, D15S984, D15S115). The analysis disclosed seven heterodisomic PWS cases originating by meiosis I (MI) ND (four showed recombination and three no recombination), and one isodisomic PWS UPD15 originating by postzygotic duplication. Among the five paternal UPD15, we detected four isodisomies, three of which showed homozigosity for all markers, corresponding to a mitotic error, and one case originating from a paternal MII ND. Our results indicate that besides maternal MI and MII ND, paternal ND occurs when a PWS UPD15 patient originates from mitotic duplication of the maternal chromosome 15. ND events in AS are mainly due to mitotic errors, but paternal MII ND can occur and give origin to an AS UPD15 individual by two different mechanisms: rescue of a trisomic fetus or fertilization of a nullisomic egg with the disomic sperm, and in this case paternal and maternal ND are necessary. Am. J. Med. Genet. 94:249–253, 2000. © 2000 Wiley‐Liss, Inc.     

Prader‐Willi syndrome genetic subtypes and clinical neuropsychiatric diagnoses in residential care adults

The historical diagnosis of Prader‐Willi syndrome (PWS), a complex genetic disorder, in adults is often achieved by clinical presentation rather than by genetic testing and thus limited genetic subtype‐specific psychometric investigations and treatment options. Genetic testing and clinical psychiatric evaluation using Diagnostic and Statistical Manual (DSM)‐IV‐TR criteria were undertaken on 72 adult residents (34 M; 38 F) from the Prader‐Willi Homes of Oconomowoc (PWHO), a specialty PWS group home system. Methylation specific‐multiplex ligation probe amplification and high‐resolution microarrays were analyzed for methylation status, 15q11‐q13 deletions and maternal uniparental disomy 15 (mUPD15). Seventy (33M; 37F) of 72 residents were genetically confirmed and 36 (51%) had Type I or Type II deletions; 29 (42%) with mUPD15 and 5 (7%) with imprinting defects from three separate families. Psychiatric comorbidities were classified as anxiety disorder (38%), excoriation (skin picking) (33%), intermittent explosive disorder ([30%‐predominantly among males at 45% compared with females at 16% [OR = 4.3, 95%CI 1.4‐13.1, P < 0.008]) and psychotic features (23%). Psychiatric diagnoses did not differ between mUPD15 vs deletion, but a greater number of psychiatric diagnoses were observed for the larger Type I (4.3) vs smaller Type II (3.6) deletions when age was controlled (F = 5.0, P < 0.04). Adults with PWS presented with uniformly higher rates of psychiatric comorbidities which differed by genetic subtype with gender‐specific trends.     

Difference in methylation patterns within the D15S9 region of chromosome 15qll–13 in first cousins with Angelman syndrome and Prader–Willi syndrome

Abnormalities of chromosome region 15qll–13 are associated with Angelman syndrome (AS) and Prader–Willi syndrome (PWS). Differences between the methylation patterns of the region of chromosome 15qll–13 which hybridizes to the highly conserved DNA, DN34, in normal individuals and in patients with AS and PWS have been described. We report on a family in which first cousins are affected by AS and PWS as a result of a familial paracentric inversion of 15qll–ql3. The results of the studies on this family demonstrate the differences in the methylation patterns in the 2 conditions and the phenomenon of genomic imprinting, whereby genetic information is expressed differently dependent on the parent of origin. © 1993 Wiley-Liss, Inc.     

Genetic variants of the human obesity (OB) gene in subjects with and without Prader—Willi syndrome: comparison with body mass index and weight

We investigated whether an association exists between genetic variants of the human obesity ( OB or leptin) gene and body mass index (BMI) or weight in subjects with Prader-Willi syndrome (PWS) and in age-and gender-matched lean and obese subjects without PWS. The study included 51 subjects with PWS (mean age = 17.7 ± 9.5 years, BMI = 29.7 ± 8.3 kg/m²); 50 non-PWS obese subjects (mean age = 18.2 ± 10.8 years, BMI = 33.3 ± 9.5 kg/m²); and 53 non-PWS lean subjects (mean age = 17.8 ± 9.5 years, BMI = 19.5 ± 2.9 kg/m²). Allele sizes were determined via standard polymerase chain reaction of the D7S1875 locus, a dinucleotide repeat polymorphism close to the OB gene and classified as trichotomous (homozygous < 208 bp, heterozygous < 208/≥ 208 bp, homozygous < 208 bp) or dichotomous (homozygous < 208 bp or not). Non-PWS males showed a marked decrease in weight with larger alleles while females did not (interaction effect, p < 0.05). Comparable effects were not observed among the PWS subjects. Associations between BMI and genotype were statistically significant (r = 0.22, one-tailed p < 0.05) and comparable to previous research among the non-PWS subjects < 18 years, but not the adults (r = 0.05, one-tailed p = 0.38). Correlations were not statistically significant among either the adult or non-adult PWS subjects.     

A variety of genetic mechanisms are associated with the Prader–Willi syndrome

An extensive set of chromosome 15 DNA polymorphisms and densitometric analysis with four markers mapping to the Prader–Willi chromosome region (PWCR) of chromosome 15 have been used to characterize a cohort of 30 subjects with classical Prader–Willi syndrome (PWS). Molecular analysis enabled the classification of the PWS subjects into four groups: (A) 18 subjects (60%) had deletions of paternal 15q11–13 involving a common set of DNA markers. Two subjects had differently sized deletions, one larger and one smaller than the other cases. (B) Eight (27%) had maternal uniparental disomy for chromosome 15. (C) One (3%) had a marker chromosome carrying an extra copy of the PWCR. The marker chromosome was demonstrated to be of paternal origin and the two intact chromosomes were maternally derived. This case represents an apparent exception to the generally held view that PWS is associated with an absence of paternally inherited gene(s) located in the PWCR. (D) The remaining three cases (10%) had none of the above abnormalities. This last subgroup of patients has not previously been well characterized but could represent limited deletions not detectable with the markers used or abnormalities in the imprinting process. These cases represent potentially valuable resources to elucidate more precisely the fundamental disorders responsible for PWS. © 1994 Wiley-Liss, Inc.     

An analytical method for the detection of methylation differences at specific chromosomal loci using primer extension and ion pair reverse phase HPLC

We have developed a rapid, accurate, and quantitative method for the detection of methylation differences at specific CpG sites based on bisulfite treatment of DNA followed by primer extension and ion-pair reversed-phase high performance liquid chromatography (IP RP HPLC). The application of the method is illustrated by analysis of differentially imprinted alleles arising from Prader-Willi and Angelman syndromes. In order to convert unmethylated cytosines to uracil, plasmid and genomic DNA samples were treated with sodium bisulfite and the targeted sequence was then amplified using oligodeoxynucleotide primers specific for the bisulfite-deaminated DNA. The PCR product(s) from this step was used as a template for a primer extension reaction and the products were subsequently analyzed chromatographically using IP RP HPLC. This method eliminates the need to use restriction enzymes to determine the methylation status of the amplicon and circumvents the need for radio labeling for the quantitative measurements. Finally, this method removes the need for nucleotide sequencing because it is not solely reliant on the presence or absence of one or more PCR products, as is the case with related methods.     

A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms

We describe a new procedure for the analysis of the methlyation status of imprinted genes based on methylation-specific PCR followed by denaturing high performance liquid chromatography (MSP/DHPLC). The method offers a rapid and very reliable alternative to conventional methods used for such purposes such as Southern blots and methylation specific PCR (allele-specific MSP). The efficient resolution of the differentially methylated alleles is demonstrated for two human imprinted genes, namely the SNRPN gene and the LIT1 gene (KCNQ1OT1). Abnormal imprinting of the two genes is associated with the Angelman/Prader-Willi syndromes and the Beckwith-Wiedemann syndrome, respectively. The MSP/DHPLC method is based on PCR amplification of gene segments which show parent-of-origin specific methylation. Genomic DNA is subjected to an in vitro bisulfite treatment prior to PCR amplifications using primers specific for modified DNA. Both alleles are theoretically amplified with equal efficiency and are represented by identically sized PCR products; they differ, however, at a number of positions within the amplified DNA segment. The DHPLC analysis allows a very efficient resolution of the two populations of PCR products. The high sensitivity and quantitative properties of the MSP/DHPLC method are illustrated based on its ability to reveal a low cell mosaicism in an infant with a maternal uniparental disomy 15 (i.e., Prader-Willi syndrome patient). The minor cell line (approximately 8% in blood) was not detectable with conventional molecular analysis. While the detection of low cell mosaicisms of structurally abnormal chromosomes usually relies on cytogenetic studies, the MSP/DHPLC method described here not only offers an alternative at the molecular level, but may also reveal mosaicisms concerning structurally intact chromosomes.     

Prevalence of pathogenic and likely pathogenic variants in the RASopathy genes in patients who have had panel testing for cardiomyopathy

RASopathies are a group of developmental disorders caused by pathogenic variants in the RAS‐MAPK pathway. Cardiomyopathy is a major feature of this group of disorders, specifically hypertrophic cardiomyopathy (HCM). HCM can be the first presenting feature in individuals with RASopathies. We conducted a retrospective study of all individuals who have had a cardiomyopathy gene panel ordered through our institution to determine the prevalence of pathogenic or likely pathogenic variants in RAS pathway genes in individuals with cardiomyopathy. We evaluated variants in the following genes: BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NF1, NRAS, PTPN11, RAF1, SHOC2, and SOS1. We reviewed 74 cases with cardiomyopathy, including 32 with HCM, 24 with dilated cardiomyopathy (DCM), nine with both left ventricular noncompaction (LVNC) and DCM, four with LVNC only, two with arrhythmogenic right ventricular cardiomyopathy (ARVC) and three with unspecified cardiomyopathy. We identified four patients (5.41%) with pathogenic or likely pathogenic variants in HRAS, PTPN11 and RAF1 (two individuals). Indication for testing for all four individuals was HCM. The prevalence of pathogenic or likely pathogenic variants in RASopathy genes in our HCM patient cohort is 12.5% (4/32). We conclude that the RASopathy genes should be included on multi‐gene panels for cardiomyopathy to increase diagnostic yield for individuals with HCM.     

Rett‐like phenotypes: expanding the genetic heterogeneity to the KCNA2 gene and first familial case of CDKL5‐related disease

Several genes have been implicated in Rett syndrome (RTT) in its typical and variant forms. We applied next‐generation sequencing (NGS) to evaluate for mutations in known or new candidate genes in patients with variant forms of Rett or Rett‐like phenotypes of unknown molecular aetiology. In the first step, we used NGS with a custom panel including MECP2, CDKL5, FOXG1, MEF2C and IQSEC2. In addition to a FOXG1 mutation in a patient with all core features of the congenital variant of RTT, we identified a missense (p.Ser240Thr) in CDKL5 in a patient who appeared to be seizure free. This missense was maternally inherited with opposite allele expression ratios in the proband and her mother. In the asymptomatic mother, the mutated copy of the CDKL5 gene was inactivated in 90% of blood cells. We also identified a premature stop codon (p.Arg926*) in IQSEC2 in a patient with a Rett‐like phenotype. Finally, exome sequencing enabled us to characterize a heterozygous de novo missense (p.Val408Ala) in KCNA2 encoding the potassium channel Kv 1.2 in a girl with infantile‐onset seizures variant of RTT. Our study expands the genetic heterogeneity of RTT and RTT‐like phenotypes. Moreover, we report the first familial case of CDKL5‐related disease.     

Comparison of the background, needs, and expectations for genetic counseling of adults with experience with Down syndrome, Marfan syndrome, and neurofibromatosis

We describe an analysis of the responses of 605 adults with experience with Down syndrome, Marfan syndrome, or neurofibromatosis (NF) to the BNE Scale, a scale specifically designed to assess the background, needs, and expectations (BNE) of genetic counseling patients. Significant group differences were found. Specifically, the respondents in the Down syndrome group reported more favorable beliefs about the condition and the availability of social support than the respondents in the other groups. Respondents in the NF group reported more unsureness about their condition and a greater need for genetic information than members of the other groups. Notably, having positive feelings about the condition was negatively correlated with support group interest for respondents of the Marfan syndrome group (r = ?0.159, P < 0.01). Having an affected child was associated with interest in health provider input (t = ?3.4; P = 0.001) and the desire to talk about psychosocial issues (t = ?2.9; P = 0.004). However, previous experience with genetic counseling was not found to affect BNE. These results support the usefulness of the BNE Scale to compare the BNE of patient groups, as well as provide important insight into the BNE of individuals seeking counseling about Down syndrome, Marfan syndrome, and NF. © 2011 Wiley‐Liss, Inc.