Exome Analysis Reveals Novel Missense and Deletion Variants in the CC2D2A Gene as Causative of Joubert Syndrome

The CC2D2A gene is essential for primary cilia formation, and its disruption has been associated with Joubert Syndrome-9 (JBTS9), a ciliopathy with typical neurodevelopmental features. Here, we describe an Italian pediatric patient with typical features of Joubert Syndrome (JBTS): “Molar Tooth Sign”, global developmental delay, nystagmus, mild hypotonia, and oculomotor apraxia. Whole exome sequencing and segregation analysis identified in our infant patient a novel heterozygous germline missense variant c.3626C > T; p.(Pro1209Leu) inherited from the father and a novel 7.16 kb deletion inherited from the mother. To the best of our knowledge, this is the first report showing a novel missense and deletion variant involving exon 30 of the CC2D2A gene.

IL12RB2 Polymorphisms correlate with risk of lung adenocarcinoma

In a previous study, lack of IL-12 signaling in il12rb2 knock-out mice was found to predispose to lung adenocarcinoma (LAC). We asked whether specific polymorphisms of the human IL12RB2 gene may confer susceptibility to LAC. We studied IL12RB2 single nucleotide polymorphisms (SNPs) spanning from the promoter to the first untranslated exon of the gene. Genotypes of 49 individuals with LAC were compared with those of 93 healthy subjects. Two allele variants were found to be associated with increased susceptibility to LAC. One haplotype (hap), hap18, was more frequent in patients (18%) versus controls (6%) and significantly associated with increased probability of disease occurrence. Furthermore, IL-12 driven STAT4 phosphorylation in T cell blasts from healthy individuals was found to correlate with both single allele variants and haplotypes. In conclusion, genetically determined low signaling activity of IL-12R predisposes to the development of LAC.

Periostin gene variants are associated with disease course and severity in juvenile idiopathic arthritis

OBJECTIVES

This study aimed to identify polymorphic variants of the Periostin gene associated with disease severity and clinical course in children with juvenile idiopathic arthritis.

METHODS

DNA genotyping of 7 single-nucleotide polymorphisms within the periostin gene was performed in 117 patients and their parents and in 102 control samples. Our patients were divided in the following 4 disease categories: 1) persistent oligoarthritis; 2) extended oligoarthritis; 3) polyarthritis; 4) systemic arthritis. Quantitative association analysis was performed in order to test for association between the 7 genetic variants and 18 selected clinical traits.

RESULTS

A harmful association was observed between the minor allele of rs17197936 and 2 clinical traits, count of joints with active arthritis and count of joints with pain on motion/tenderness, in patients with extended oligoarthritis. Furthermore, the haplotype represented by the minor allele variants of rs3829364, rs6750 and rs9547951 showed an unfavourable association with the above 2 traits plus the following 3 in the whole patient group: juvenile arthritis damage index articular score, childhood health assessment questionnaire score and disease duration.

CONCLUSIONS

These associations suggest that the variants involved can be regarded as genetic factors influencing some phenotypic aspects of juvenile idiopathic arthritis. Genotyping of this gene may represent a useful tool to identify patients who are at greatest risk of experiencing a poorer long-term outcome.

Sex chromosome rearrangements leading to partial aneuploidies and mosaicisms: use of QF-PCR for detection and quantification of the involved cell lines

Chromosome rearrangements can lead to aneuploidies of specific chromosome regions and could be present in the entire individual or limited to some tissues (mosaicism) depending on the developmental stage of the embryo when the rearrangement occurs. We report 6 cases with sex chromosome rearrangements identified by conventional cytogenetics and tested by quantitative fluorescent polymerase chain reaction (QF-PCR). QF-PCR has been largely employed for rapid detection of common aneuploidies in pre-natal and post-natal diagnosis and consists in DNA amplification by polymerase chain reaction (PCR) using fluorescent labelled primers and the analysis of chromosome specific small tandem repeats (STR). We tested 5 sex chromosome specific STR markers in multiplex PCR amplifications together with other chromosome specific STR markers as control amplifications. The PCR products were analysed by capillary electrophoresis. The results from QF-PCR analysis were obtained within one day and confirmed our cytogenetic observations. This study shows that QF-PCR analysis can detect sex chromosome imbalance and also suspect mosaicism or chromosome rearrangement.

A report on 528 intragenic deletions detected in DMD and BMD patients by an Italian collaborative study

The results of a collaborative study involving about one third of the total DMD and BMD cases living in the Italian territory are reported. The analysis of the breakpoint frequency by intron revealed significant differences among regional groups of DMD patients (for introns 2, 11 and 50 in Sardinia and for introns 9 and 45 in northeastern Italy), whereas no regional differences were observed among regional groups of BMD patients. These differences involve the same Italian regions which previous studies, performed by different markers, identified as "genetically differentiated". The data support the possibility of a differential distribution among populations of some intronic sequences, facilitating the origin of deletion breakpoints within the dystrophin gene.

Deleted and normal chromosome 10 homologs from a patient with Hirschsprung disease isolated in two cell hybrids through enrichment by immunomagnetic selection

A cytogenetically detectable deletion, del(10) (q11.2-->q21.2), was observed in a patient with total colonic aganglionosis with small bowel involvement (TCSA), a variant of Hirschsprung disease (HSCR). A similar deletion is present in another TCSA patient (S.M. Huson, personal communication). To reveal cytogenetically undetectable deletions of chromosome 10 in further patients, we developed a strategy for mapping chromosome 10 DNA markers with respect to the observed deletions. To this end, the two chromosome 10 homologs (deleted and normal) were segregated in two distinct somatic cell hybrids obtained after fusion of the patient's fibroblasts with a Chinese hamster ovary cell line (YH21). Hybrid cells containing chromosome 10 were selected for the expression of the gene coding for the beta subunit of the fibronectin receptor (FNRB), which maps to 10p11.2, using a monoclonal antibody against FNRB. Hybrid 185.O contains the deleted chromosome, whereas hybrid 179.Q contains the nondeleted one. Southern blot and PCR analysis of DNA from these two hybrids mapped the markers RBP3H4, RET, D10S15, D10S5, D10S22, and D10S88 inside the deletion and D10S170, CDC2, EGR2, and D10S19 outside the deletion. MEN2A and MEN2B have recently been mapped within the centromeric region closely linked to RBP3 and D10S15 (which are located inside the deletion) and cosegregate with HSCR in at least two different pedigrees. Since HSCR, MEN2A, and MEN2B represent defects of neural crest cell development, we hypothesize that they originate from mutations in different genes clustered in the centromeric region of 10q.

Screening Duchenne and Becker muscular dystrophy patients for deletions in 30 exons of the dystrophin gene by three-multiplex PCR

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Diagnosis of Duchenne and Becker muscular dystrophies by polymerase chain reaction. A multicenter study

OBJECTIVE--To assess the efficiency, reliability, and ease of use of DNA diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) using the polymerase chain reaction (PCR). DESIGN--DNA from the patients was screened for deletion mutations using multiplex PCR, and the results were compared with those obtained by Southern blot analysis. The PCR multiplex reaction detects nine specific "hot-spot" exons in the dystrophin gene while the Southern analysis detects 66 specific dystrophin gene restriction fragments. The multiplex reaction requires 50-fold less DNA than Southern analysis and thus is considerably more sensitive. SETTING--Fourteen university-affiliated and private genetic disease diagnostic laboratories. PATIENTS--Male patients with clinical signs of DMD/BMD. Cases were selected for analysis randomly, without knowledge of whether a deletion was present within the dystrophin gene. MAIN OUTCOME MEASURES--The percentage of cases that were detectable by multiplex PCR in comparison with Southern analysis, the frequency, extent, and location of the detected deletion mutations. In some cases, duplication mutations were monitored. RESULTS--The accuracy of a single PCR multiplex amplification (nine exons) was compared with Southern analysis with 10 cDNA probes that cover the full length of the gene. The multiplex PCR analytic method detected 82% of those deletions detected by Southern analysis methods. In one of 745 analyses, the multiplex method suggested a single exon deletion, which was not confirmed by Southern analysis, representing a false-positive rate of 0.013%. CONCLUSIONS--Multiplex PCR represents a sensitive and accurate method for deletion detection of 46% of all cases of DMD/BMD. The method requires 1 day for analysis, is easy to perform, and does not use radioactive tracers. As such, multiplex PCR represents an efficient and rapid method for prenatal or postnatal diagnosis of DMD/BMD.

Parental origin and germline mosaicism of deletions and duplications of the dystrophin gene: a European study

Knowledge about the parental origin of new mutations and the occurrence of germline mosaicism is important for estimating recurrence risks in Duchenne (DMD) and Becker muscular dystrophy (BMD). However, there are problems in resolving these issues partly because not all mutations can as yet be directly detected, and additionally because genetic ratios are very sensitive to ascertainment bias. In the present study, therefore, analysis was restricted to currently detectable mutations (deletions and duplications) in particular types of families which tend to be rare. In order to obtain sufficient data we pooled results from 25 European centers. In mothers of affected patients who were the first in their family with a dystrophin gene deletion or duplication, the ratio between the paternal and the maternal origin of this new mutation was 32:49 (binomial test P = 0.075) for DMD. In five BMD families the ratio between paternal and maternal origin of new mutations was 3:2. Recurrence risk because of maternal germline mosaicism was studied in sisters or subsequent sibs of isolated cases with an apparently new detectable mutation. In 12 out of 59 (0.20; 95% CI 0.10-0.31) transmissions of the risk haplotype the DMD mutation was transmitted as well. No recurrences were found in nine BMD families.

Genotype-phenotype correlation and germline mosaicism in DMD/BMD patients with deletions of the dystrophin gene

The molecular analysis of 127 DMD/BMD patients showed that 73 of them (57%) had deletions in the dystrophin gene. Two different methods were used in this study: (a) hybridization of HindIII-digested genomic DNA with nine cDNA probes corresponding to the entire 14kb cDNA of the DMD gene; and (b) simultaneous amplification of nine exons of the DMD gene (multiplex DNA amplification) by the polymerase chain reaction (PCR). When the deletion breakpoints of the intragenic deletions were analyzed with regard to their phenotypic consequences, nine patients were found to represent exceptions to the reading-frame hypothesis. Information regarding mental development was also available for 61 of the 73 deleted patients and for 34 of the 54 non-deleted ones. The proportion of mentally retarded patients was found to be similar in the two groups (deleted, 15%; non-deleted, 18%). Finally, in one family, a junction fragment present in the patient was not found in the peripheral blood DNA of the mother but was present in the sister, thus indicating germline mosaicism in the mother.

The molecular basis for Duchenne versus Becker muscular dystrophy: correlation of severity with type of deletion

About 60% of both Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) is due to deletions of the dystrophin gene. For cases with a deletion mutation, the "reading frame" hypothesis predicts that BMD patients produce a semifunctional, internally deleted dystrophin protein, whereas DMD patients produce a severely truncated protein that would be unstable. To test the validity of this theory, we analyzed 258 independent deletions at the DMD/BMD locus. The correlation between phenotype and type of deletion mutation is in agreement with the "reading frame" theory in 92% of cases and is of diagnostic and prognostic significance. The distribution and frequency of deletions spanning the entire locus suggests that many "in-frame" deletions of the dystrophin gene are not detected because the individuals bearing them are either asymptomatic or exhibit non-DMD/non-BMD clinical features.

Analysis of peripheral maternal blood samples for the presence of placenta-derived cells using Y-specific probes and McAb H315

Using flow cytometry, a small number of cellular elements expressing on their surface an antigen (H315) produced by placental trophoblast have been observed in the peripheral blood of pregnant women. This is in agreement with previous observations (Covone et al., 1984a,b) and recent results documenting the presence of a small number of H315-positive cells in the peripheral circulation of pregnant women (Pool et al., 1987; Caligaris-Cappio and Camaschella, personal communication). When DNA extracts, prepared from H315-positive cells sorted from maternal samples were tested by Southern transfer using Y-specific probes (Y190 or Y411), a Y-specific band could not be detected in any sample analysed, irrespective of the sex of the fetus. In control samples from healthy male donors, a Y-specific band could be detected with as few as 800 46,XY cells without interference from contaminating 46,XX cells. H315-positive cellular elements, sorted by flow cytometry from the maternal peripheral blood, were also examined in interphase using Y-specific probes (Y190 and Y431) and an in situ biotin-avidin fluorescent hybridization technique. The great majority of the sorted H315-positive cellular elements did not show a fluorescent Y body, even in samples from mothers who later delivered a male infant. While previous investigations had failed to demonstrate the in vitro uptake of H315 antigen onto the surface of leucocytes from healthy males incubated in maternal sera, the present studies demonstrate that cells from male donors could adsorb this antigen following incubation in extracts prepared from retroplacental blood. These findings thus suggest that the majority of H315-positive nucleated cells previously detected by flow cytometry in the peripheral circulation of pregnant women are maternal cells which have adsorbed H315 antigen in vivo, either in soluble form or as small cell membrane fragments.

Identification of trophoblast in chorionic villi biopsy samples

We have investigated a test for rapid discrimination between foetal and maternal origin of chorionic villi biopsy samples. A monoclonal antibody named H315 reacting against a specific antigen present on the surface of foetal trophoblastic cells, plus a double-colour staining technique (FITC + PI), have been used for the identification of foetal cells (H315-positive) and for visualization of nucleate (PI-positive) and anucleate (PI-negative) structures of chorionic villi. This test could be useful in differentiating foetal and maternal cells in chorionic villi biopsy samples currently used for prenatal diagnostic purposes.

Trophoblast cells in peripheral blood from pregnant women

The presence of human trophoblast cells in maternal blood was investigated by the use of flow cytometry and a monoclonal antibody reacting against a specific antigen present on the surface of these cells. Three types of cells derived from the placenta could be detected in the peripheral blood obtained from women between 6 weeks' gestation and term. One group of cells were polynucleated, a second group were diploid, and a third consisted of anucleate cells derived from the syncytiotrophoblast. These cells should be suitable for prenatal diagnosis of chromosomal and biochemical abnormalities.