Survey of medical genetic services in Italy: year 2011.

BACKGROUND: The aim of this study was to collect information about 2011 genetic activities in Italy, with the purpose of providing guidance to the national health systems in order to improve genetic services. METHODS: A web-based survey was carried out to achieve the information. RESULTS: Data were collected from 268 macrostructures hosting 517 services and employing 3246 persons. About 295,000 cytogenetic, 35,000 immunogenetic and 263,000 molecular genetic analyses of 902 genes were recorded. Seventy-four percent of the services were accredited with institutional bodies and 57 % were also certified according to ISO 9001 standard. Twenty percent of cytogenetic laboratories had participated in an European External Quality Assessment (EQA) while 44 % participated in a national EQA. Only 28 % of the molecular laboratories had participated in a national Cystic Fibrosis EQA. The percentage of diagnoses confirmed by genetic tests varied among disorders, ranging from 52 % for coeliac disease to 4 % for fragile X syndrome. CONCLUSIONS: This study highlights the need for reorganizing the Italian genetic services network, improving EQA participation and developing national plans for implementing next generation technologies. Concerted effort has to be addressed in the education of the professionals prescribing tests to improve appropriateness and to inform patients, who now have exposure to direct-to-consumer multifactorial genetic testing where clinical utility is unproven.

Robert J. Gorlin: Personal Memory of a Friend and Mentor in Clinical Genetics.

Robert J [...].

The difficult nosology of blepharophimosis-mental retardation syndromes: report on two siblings.

Blepharophimosis-mental retardation syndromes (BMRS) include a group of clinically and etiologically heterogeneous conditions, which can occur as isolated features or as part of distinct disorders displaying multiple congenital anomalies. We report on two siblings, a 6-year-old girl and an 18-month-old male, presenting with overlapping clinical findings. Major characteristics included facial dysmorphisms with upward slanted palpebral fissures, blepharophimosis, telecanthus, hypertelorism, posteriorly rotated and abnormal ears, and micrognathia. Ectodermal abnormalities consisted of fine hair, sparse eyebrows, and thin skin. Both patients had feeding difficulties with gastro-esophageal reflux and growth retardation. Psychomotor skills were severely delayed with no verbal capacity. The male sib also displayed low growth hormone (GH) levels, while the older sister had low cholesterol and mildly elevated TSH levels. Numerous metabolic/genetic investigations, including cholesterol precursors, dosage, and high-resolution array-CGH, were negative. BMR syndromes, including Dubowitz syndrome, Marden-Walker syndrome, Ohdo/Ohdo-like syndromes, and the cholesterol storage disorders were considered. We concluded that these two patients are affected by a possible autosomal recessive condition within the heterogeneous clinical spectrum of BMRS, fitting with the Young-Simpson syndrome subtype.

TBX2 gene duplication associated with complex heart defect and skeletal malformations.

We report on a patient with mild mental retardation, prenatal onset growth retardation, cerebellar hypoplasia, and complex heart defect including: interventricular septal defect, patent foramen ovale, aortic coarctation, tricuspid valve insufficiency, mitral valve stenosis, and minor skeletal anomalies with hypo-aplasia of the distal phalanges. A SNP-array analysis detected a de novo duplication of 17q23.2, encompassing the TBX2 gene. Animal models argue for a key role of Tbx2 during cardiac and limb development. Accordingly, we hypothesize that the heart malformation and mild digital anomalies found in this patient could be related to TBX2 gene overexpression, suggesting parallel consequences of TBX2 gene dosage imbalances in animals and in humans.

3q29 Microdeletion: a mental retardation disorder unassociated with a recognizable phenotype in two mother-daughter pairs.

The 3q29 microdeletion syndrome (del 3q29) is a novel genomic disorder identified after the introduction of microarray-based technology. The phenotype of the reported patients is variable, including mental retardation and subtle facial anomalies. We report on two mother-daughter pairs, heterozygous for 3q29, and review clinical features of all known affected individuals. Del 3q29 syndrome is associated with nonspecific clinical features, including mild-to-moderate developmental delay, microcephaly, and mild facial dysmorphisms such as short philtrum and high nasal bridge. Facial anomalies were nonoverlapping and nondistinct, also within each mother-daughter pair. Parental transmission of del 3q29 could be more frequent than previously considered. Malformations are rare, occurring only in single subjects. The phenotypic diversity of affected patients and the lack of distinct dysmorphisms suggest that this disorder cannot be recognized on clinical ground alone. Del 3q29 should be searched in subjects with unexplained mild/moderate mental retardation, microcephaly, and minor nonspecific facial anomalies.

Compound heterozygosity for GDF5 in Du Pan type chondrodysplasia.

Du Pan type chondrodysplasia (DPC) represents the milder end of homozygous growth differentiation factor 5 (GDF5) disorders. We report on a 20-month-old child with complex brachydactyly and mild proximal fibular hypoplasia, consistent with DPC, in the absence of other anomalies of long bones and joints. Mutational analysis disclosed two novel GDF5 mutations within the protein's mature domain and in the cleavage site of the prodomain which explains the distinct DPC phenotype found in this patient. The unaffected mother and the father who presented with mild brachybaso/mesophalangy of all digits were both heterozygous carriers.

Complex rearrangement of chromosomes 7q21.13-q22.1 confirms the ectrodactyly-deafness locus and suggests new candidate genes.

Complex chromosomal rearrangements with more than two breakpoints are rare. We report on a 5-year-old girl, evaluated because of psychomotor delay, ectrodactyly of right hand and feet, craniofacial dysmorphic features, cleft palate, deafness, and tetralogy of Fallot. A standard karyotype suggested a small intrachromosomal duplication of chromosome 7q. The chromosomal rearrangement was characterized by mBAND, which disclosed a reciprocal interstitial translocation t(7;8)(q21q22;q23q24). FISH analysis and array-CGH analysis showed a paracentric inversion of 7q and a microdeletion of 7q21.13. The parents had normal chromosomes. The deletion found in the present patient confirms that candidate region of ectrodactyly-deafness (OMIM 220600) maps to 7q21 and suggests new candidate genes for that disorder. This patient also had facial features reminiscent of tricho-rhino-phalangeal syndrome and one chromosome breakpoint involved band 8q24, a locus for this disorder. In addition, FOG1 gene maps to 8q23 and has been implicated in a subset of subjects with tretralogy of Fallot. We suggest that the aberration of 8q may have contributed to her facial and cardiac findings.

Syndromic craniosynostosis due to complex chromosome 5 rearrangement and MSX2 gene triplication.

Craniosynostosis is a common birth defect ( approximately 1/3,000 births) resulting from chromosome imbalances, gene mutations or unknown causes. We report a 6-month-old female with multiple sutural synostosis and prenatal onset growth deficiency, developmental delay, facial dysmorphism, congenital heart defect, and inguinal hernia. An integrated approach of standard cytogenetics, mBAND, locus-specific FISH, and 75 kb resolution array-CGH disclosed a complex chromosome 5 rearrangement, resulting in 3 paracentric inversions, 2 between-arm insertions, and partial duplication of 5q35. An extra copy of the MSX2 gene, which maps within the duplicated segment and is mutated in Boston-type craniosynostosis, was confirmed by molecular cytogenetic studies. Our study confirms that early fusion of cranial sutures commonly observed in the dup(5q) syndrome is caused by triplication of the MSX2 gene and strongly supports the crucial role of this gene in the development of craniofacial structures.

Genetic testing in Italy, year 2004.

A comprehensive and long-range monitoring of genetic testing is ongoing in Italy starting from 1987. The data collected by the last survey of year 2004, on behalf of the Italian Society of Human Genetics, included the activities of 88 clinical centres and 160 cytogenetic and 183 molecular genetic laboratories, hosted by 256 structures. Only 42% of them fulfilled the requirements of current Italian legislation. Genetic tests included 283,601 cytogenetic analyses. There have been 120,238 invasive prenatal samplings, 84% of which were amniocenteses. A significant north-to-south decreasing gradient was evident for all activities. This study has also surveyed 190,610 molecular genetic tests. CFTR gene analysis accounted for 23% of prenatal and 29% of postnatal molecular tests. In total, 420 different genes have been investigated, 10 of which comprised three-quarters of the whole activity. More than 10% of molecular tests were performed on fetal samples, the analysis of CFTR, DMD, FMR1, FMR2, and GJB2 genes accounting for 83% of all prenatal tests. In years 1997-2004, the demand of cytogenetic tests has increased two-fold and that of molecular tests has increased four-fold. Only 16% of cytogenetic and 12.5% of molecular tests have been followed by genetic counselling. This survey highlights the need for a major basic intervention in the general organisation of genetic structures in Italy, which should be rationalised in accordance with the national guidelines, and the necessity of constant training of general practitioners and education of consumers to the appropriate use of genetic testing.

Novel EXT1 and EXT2 mutations identified by DHPLC in Italian patients with multiple osteochondromas.

We describe the results of an optimised DHPLC-based mutation screening of the EXT1 and EXT2 genes in Italian patients affected by multiple osteochondromas [MO; also referred to as hereditary multiple exostoses (HME) in the literature], using a multistep approach. We first analysed 36 unrelated probands for EXT1 mutations by DHPLC analysis and subsequent direct sequencing of all samples with abnormal elution profile. Negative cases were then screened for EXT2 mutations using the same approach. In patients who tested normal at DHPLC screening, all EXT1 and EXT2 exons and splice-site junctions were directly sequenced. In 7 informative families, we also performed a pre-screening linkage analysis to selectively focus the DHPLC testing on the EXT1 or EXT2 gene. We detected 31 MO-related mutations, of which 23 (74%) were novel. Seven polymorphisms were also found. Twenty-four mutations (77%) were found in EXT1 and 7 (23%) in EXT2. No disease-causing mutations were detected in five of 36 patients, with a mutation frequency of 86%. According with previous studies, most mutations (90%) are loss of function. Neither false positive nor false negative results were obtained. This multistep method can be considered a fast and reliable diagnostic strategy for the detection of EXT1/2 mutations, with excellent sensitivity and specificity.

A homozygous GJA1 gene mutation causes a Hallermann-Streiff/ODDD spectrum phenotype.

Oculodentodigital dysplasia (ODDD) and Hallermann-Streiff syndrome (HSS) share several clinical characteristics. However, while ODDD is a dominantly inherited disorder due to mutations in the connexin 43 gene GJA1, the inheritance pattern of the HSS syndrome is still debated. Overlapping phenotypes have been described. In one of such cases we found a homozygous change at the very conserved R76 codon (c.227G>A, p.R76H), the clinically normal parents being heterozigous carriers of the same mutation. A different base change at the same codon (p.R76S) leads to a complete dominant ODDD phenotype. A case of full-blown HSS phenotype was also analysed but GJA1 mutations were not found. GJA1 homozygous hypomorphic mutations can result in a phenotype in the HSS/ODDD spectrum.

NF1 gene analysis based on DHPLC.

The high mutation rate at the NF1 locus results in a wide range of molecular abnormalities. The majority of these mutations are private and rare, generating elevated allelic diversity with a restricted number of recurrent mutations. In this study, we have assessed the efficacy of denaturing high-performance liquid chromatography (DHPLC), for detecting mutation in the NF1 gene. DHPLC is a fast and highly sensitive technique based on the detection of heteroduplexes in PCR products by ion pair reverse-phase HPLC under partially denaturing conditions. We established theoretical conditions for DHPLC analysis of all coding exons and splice junctions of the NF1 gene using the WAVEmaker software version 4.1.40 and screened for mutations a panel of 40 unrelated NF1 patients (25 sporadic and 15 familial), genetically uncharacterized. Disruptive mutations were identified in 29 individuals with an overall mutation detection rate of 72.5%. The mutations included eight deletions (exons 4b, 7, 10a, 14, 26, and 31), one insertion (exon 8), nine nonsense mutation (exons 10a, 13, 23.1, 27a, 29, 31, and 36), six missense mutations (exons 15, 16, 17, 24, and 31), four splice errors (exons 11, 14, 36, and 40) and a complex rearrangement within exon 16. Eighteen (62%) of the identified disruptive mutations are novel. Seven unclassified and three previously reported polymorphisms were also detected. None of the missense mutations identified in this study were found after screening of 150 controls. Our results suggest that DHPLC provides an accurate method for the rapid identification of NF1 mutations.

Ten novel mutations in the human neurofibromatosis type 1 (NF1) gene in Italian patients.

The entire NF1 coding region was analyzed for mutations in a panel of 108 unrelated Italian NF1 patients. Using PTT, SSCP, and DNA sequencing, we found 10 mutations which have never been reported before. Clinical diagnosis of NF1 was established according to the NIH consensus criteria in 100 individuals, while 8 were young children with only multiple cafè-au-lait spots. We detected 46 truncated fragments, and 24 of them were fully characterized by SSCP and direct sequencing. Of the 24, 14 were known mutations (R304X, R681X, Q682X, R1306X, R1362X, R1513X, R1748X, Q1794X, R1947X, Y2264X, R2237X, 2674delA, 6789delTTAC, 2027insC). The other 10 mutations represent novel changes that contribute to the germline mutational spectrum of the NF1 gene (K810X, Q2595X, 6772delT, 7190delCT, 7331delA, 1021insTT, 3921insT, 4106insTA, 7149insC, 2033insCG / 2034delA). PTT in a large number of Italian NF1 patients supports the usefulness of this method for characterization of mutations in disorders where the responsible gene is very large and the disease-causing mutations often create a stop codon. In agreement with previous reports, no mutational hotspots within the NF1 gene were detected.

Recurrent triploidy of maternal origin.

Triploidy is the most frequent chromosome aberration in first trimester spontaneous abortions. In contrast to aneuploidies due to nondisjunction, increased maternal age is not a risk factor and the mechanism of triploidy remains poorly understood. To date, recurrence of triploidy of maternal origin has been described only in a few families suggesting some underlying genetic factors. Here, we report on a woman who underwent three consecutive triploid pregnancies, in two of which maternal origin of triploidy was proved by molecular analysis.

A novel PTPN11 gene mutation bridges Noonan syndrome, multiple lentigines/LEOPARD syndrome and Noonan-like/multiple giant cell lesion syndrome.

Noonan (NS) and multiple lentigines/LEOPARD syndromes (LS) have proved to be associated with distinct PTPN11 mutations. Noonan-like/multiple giant cell lesion syndrome (NLS) is a rare disease, characterised by short stature, facial dysmorphisms, congenital heart defect (CHD) and central giant cell lesions. PTPN11 gene mutations have been reported in a single NLS family and two sporadic patients. Here we report a patient with a complex phenotype progressing throughout the years from NS at birth towards LS and NLS. PTPN11 gene analysis disclosed a novel missense mutation (Ala461Thr) in exon 12, affecting the consensus sequence of the SHP2-active site. This observation joins together NS and LS to NLS into a unique genetic defect, broadening the clinical and molecular spectrum of PTPN11-related disorders.

DiGeorge subtypes of nonsyndromic conotruncal defects: evidence against a major role of TBX1 gene.

The role of the 22q11 region genes, and among them TBX1, in nonsyndromic conotruncal defects (CTDs) is still unclear. Mice hemizygous at the Tbx1 locus show a remarkable incidence of heart outflow tract anomalies, of the same type commonly found in DiGeorge/Velo-cardio-facial syndrome (DGS/VCFS). Mutation analysis of the TBX1 gene in isolated, nonsyndromic CTDs has not demonstrated any functional pathogenetic variation so far. We screened the TBX1 gene in 41 patients affected by nonsyndromic CTDs of the DGS/VCFS subtype, principally "atypical" tetralogy of Fallot. Besides a few polymorphisms, we did not find any pathogenetic variation. These results do not support a major role of the TBX1 gene as responsible for human nonsyndromic CTDs.

Primary hypothyroidism and osteopenia associated with Neuhauser syndrome.

We report on a patient affected by Neuhauser megalocornea-mental retardation (MMR) syndrome, presenting with most of the major manifestations of this disorder, in association with primary hypothyroidism and osteopenia. These symptoms, previously reported in single patients, could be discrete features of MMR syndrome.

Fluorescence in situ hybridization analysis of allelic losses involving the long arm of chromosome 17 in NF1-associated neurofibromas.

Neurofibromatosis type 1 (NF1) is a common autosomal dominant condition associated with germline mutations of the NF1 gene located at chromosome band 17q11.2. Molecular analysis of a number of NF1-specific tumors has shown the inactivation of both NF1 alleles during tumorigenesis, supporting the tumor suppressor hypothesis for the NF1 gene. Using interphase dual-color fluorescence in situ hybridization (FISH) technique on paraffin-embedded tissues, we studied 11 plexiform, 4 cutaneous, and 6 subcutaneous neurofibromas. Cytogenetic analysis was conducted using two probes, one specific for the NF1 region (RP11-229K15) and one for the centromeric region of chromosome 17 as control. No large somatic deletions were found. Only in one of the plexiform neurofibromas loss of a whole chromosome 17 was observed. If we assume that dual-color FISH analysis is sensitive enough to detect the majority of large somatic deletions present, then other mutational mechanisms affecting the NF1 gene are probably involved in neurofibroma formation, and other tumor suppressor genes may play an important role in NF1 tumorigenesis.