Genetic tests for low- and middle-income countries: a literature review.

The aim of this review is to describe a series of ten genetic diseases with Mendelian inheritance pattern in people of low- or middle-income countries, which can be easily identified with simple and affordable methods. Recent information shows that although genetic diseases account for more than 10% of infant mortality in such countries, testing, counseling, and treatment of genetic diseases is not a priority. The selection criteria for the genetic tests that are discussed in this review are: i) the frequency of the genetic disease in the general population, ii) the cost and ease of execution, and iii) the report of validated methods in the literature for the diagnosis of these diseases. The goal is to promote diagnosis of genetic diseases at low-cost and with relative ease, thereby enabling appropriate treatments, reducing mortality, and preventing genetic diseases in high-risk families.

CircRNAs in hematopoiesis and hematological malignancies.

Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.

A Rare Case of Emberger Syndrome Caused By a De Novo Mutation in the GATA2 Gene.

Emberger syndrome, or primary lymphedema with myelodysplasia, is a severe rare disease characterized by early primary lymphedema and blood anomalies including acute childhood leukemia. The syndrome is associated with heterozygous mutations in the GATA2 gene. We report on a 13-year-old boy who developed lymphedema of the right lower limb at age 6 years which was accompanied by severe panleukopenia and repeated episodes of erysipelas. The suspicion of Emberger syndrome was confirmed by detection of a new germinal line GATA2 mutation c.414_417del, p.Ser139Cysfs*78. Clinical treatment included a bone marrow transplant from the father.This case is one of a very limited number of Emberger syndrome cases documented in the literature, and genetic testing proved fundamental for definition of the condition and its association with a de novo mutation in the GATA2 which is reported here for the first time.

Epidemiology and a novel procedure for large scale analysis of CFTR rearrangements in classic and atypical CF patients: a multicentric Italian study.

BACKGROUND: Mutation epidemiology in each ethnic group is a crucial step of strategies for cystic fibrosis (CF) diagnosis and counselling. To date, the scanning of the whole coding region of the cystic fibrosis transmembrane conductance regulator (CFTR) gene permits to identify about 90% of alleles from patients bearing CF and a lower percentage in patients bearing atypical CF. CFTR rearrangements in heterozygosis elude current techniques for molecular analysis, and some of them have been reported with a frequency up to 6% in various ethnic groups. METHODS: Using quantitative PCR analysis of all coding regions, we assessed the occurrence of CFTR rearrangements in 130 alleles from classic CF patients and in 198 alleles from atypical CF patients (all unrelated and from Italian descent) bearing unidentified mutations after the scanning of CFTR. RESULTS: Seven rearrangements (i.e., dele1, dele2, dele2_3, dele 14b_17b, dele17a_18, dele22_23, and dele22_24) were identified in 34/131 (26.0%) CF alleles bearing undetected mutations (which means about 2.5% of all CF alleles) and in none of the 198 alleles from atypical CF. The CFTR haplotype and the sequence analysis of the breakpoints confirmed the common origin of all the rearrangements. Thus, we set up a novel duplex PCR assay for the large-scale analysis of the seven rearrangements. The procedure was rapid (all PCR amplifications were obtained under the same conditions), costless and repeatable. CONCLUSIONS: It is useful to select the CFTR rearrangements more frequent in specific ethnic groups and to set up procedures for large-scale analysis. Their study can be performed in cases in which a high detection rate is required (i.e., partners of CF carriers/patients). On the contrary, the analysis of rearrangement is useless in atypical CF patients.

Highly preferential association of NonF508del CF mutations with the M470 allele.

BACKGROUND: On the basis of previous findings on random individuals, we hypothesized a preferential association of CF causing mutations with the M allele of the M470V polymorphic site of the CFTR gene. METHODS: We have determined the M/V-CF mutation haplotype in a series of 201 North East Italian and 73 Czech CF patients who were not F508del homozygotes, as F508del was already known to be fully associated with the M allele. RESULTS: Out of 358 not F508del CF genes, 84 carried the V allele and 274 the less common M allele. In the N-E Italian population, MM subjects have a risk of carrying a CF causing mutation 6.9x greater than VV subjects when F508del is excluded and 15.4x when F508del is included. In the Czech population a similar, although less pronounced, association is observed. CONCLUSIONS: Besides the possible biological significance of this association, the possibility of exploiting it for a pilot screening program has been explored in a local North East Italian population for which CF patients were characterized for their CF mutation. General M470V genotyping followed by common CF mutation screening limited to couples in which each partner carries at least one M allele would need testing only 39% of the couples, which contribute 89% of the total risk, with a cost benefit.

Heparan sulfate glycosaminoglycans are receptors sufficient to mediate the initial binding of adenovirus types 2 and 5.

Cell infection by adenovirus serotypes 2 and 5 (Ad2/5) initiates with the attachment of Ad fiber to the coxsackievirus and Ad receptor (CAR) followed by alpha(v) integrin-mediated entry. We recently demonstrated that heparan sulfate glycosaminoglycans (HS GAGs) expressed on cell surfaces are involved in the binding and infection of Ad2/5 (M. C. Dechecchi, A. Tamanini, A. Bonizzato, and G. Cabrini, Virology 268:382-390, 2000). The role of HS GAGs was investigated using extracellular soluble domain 1 of CAR (sCAR-D1) and heparin as soluble receptor analogues of CAR and HS GAGs in A549 and recombinant CHO cell lines with differential levels of expression of the two receptors and cultured to various densities. Complete inhibition of binding and infection was obtained by preincubating Ad2/5 with both heparin (10 microg/ml) and sCAR-D1 (200 microg/ml) in A549 cells. Partial inhibition was observed when heparin and sCAR-D1 were preincubated separately with Ad. The level of heparin-sensitive [(3)H]Ad2/5 binding doubled in sparse A549 cells (50 to 70,000 cells/cm(2)) with respect to that of cells grown to confluence (200 to 300,000 cells/cm(2)), in parallel with increased expression of HS GAGs. [(3)H]Ad2 bound to sparse CAR-negative CHO cells expressing HS GAGs (CHO K1). No [(3)H]Ad2 binding was observed in CHO K1 cells upon competitive inhibition with heparin and in HS GAG-defective CHO A745, D677, and E606 clones. HS-sensitive Ad2 infection was obtained in CAR-negative sparse CHO K1 cells but not in CHO A745 cells, which were permissive to infection only upon transfection with CAR. These results demonstrate that HS GAGs are sufficient to mediate the initial binding of Ad2/5.

A 1.1-kb duplication in the p67-phox gene causes chronic granulomatous disease.

Chronic granulomatous disease (CGD) is a rare inherited immunodeficiency that is caused by a functional defect of the NADPH oxidase of phagocytes, and that leads to severe recurrent infections. CGD results from the absence or the dysfunction of various components of NADPH oxidase, and autosomal recessive CGD with the lack of p67-phox (A67 CGD) is the rarest form of the disease. Identifying familiar mutations in subjects with A67 CGD provides the most reliable method of detecting carriers and is the basis for prenatal diagnosis. In the present study, we report the detailed characterization of the first duplication in the p67-phox gene identified in a 30-year-old patient affected by systemic aspergillosis attributable to p67-phox deficiency. We show that this new mutation involving exons 9 and 10 is the result of a tandem duplication of approximately 1.1 kb, which resulted from the juxtaposition of intron 8 to intron 10. We have sequenced both the junction fragment of this duplication and the corresponding wild-type regions and have found that the breakpoint regions in intron 8 and in intron 10 show limited homology. Our result suggests that this interchange arose as an illegitimate recombination event. As in other non-homologous rearrangements previously reported, the duplication breakpoints are located within the sequence motif 5'-CCAG-3' and its complement 5'-CTGG-3'.

Analysis of the entire coding region of the cystic fibrosis transmembrane regulator gene in idiopathic pancreatitis.

Many Cystic Fibrosis (CF) carriers have been detected testing some subjects with chronic pancreatitis for a limited number of mutations. The aim of this study was to find out if some subjects with pancreatitis and a CFTR mutation actually carry another, undetected mutation. We screened for 18 CFTR mutations plus the CFTR intron 8 poly(T) tract length a population of 67 patients suffering from idiopathic either acute, or recurrent acute, or chronic pancreatitis. Three of them were diagnosed as affected by CF. Among the others, a subset of 14 (8 CFTR mutation carriers, 4 5T carriers, and 2 sweat chloride borderliners) was selected and analyzed by denaturing gradient gel electrophoresis. Six possibly CF-related mutations were detected: L997F and 3878delG were found in two of the subjects already carrying another mutation, S1235R and L997F in one patient carrying the 5T, and L997F and D614G in the two patients with borderline sweat chloride. Among the 14 selected cases a total of 11 patients carried at least one mutation, and three of them were compound heterozygotes. Though it is debatable whether these three individuals can be considered affected by CF, their pancreatitis is possibly a clinical manifestation of some CFTR-related disease. Hum Mutat 18:166, 2001.

Heparan sulfate glycosaminoglycans are involved in adenovirus type 5 and 2-host cell interactions.

Gene therapy vectors derived from subgroup C adenoviruses of the serotype 5 (Ad5) and 2 (Ad2) resulted in inefficient infection of well differentiated respiratory cells, both in vitro and in vivo. The level of expression and localization of the primary receptor for Ad5 and Ad2, termed CAR, do not completely explain why the infection efficiency varies greatly in different experimental conditions. The possibility that additional receptors like proteoglycans are involved in the infection of Ad5 and Ad2 was investigated, because several pathogenic microorganisms use heparan sulfate-glycosaminoglycans (HS-GAGs) as coreceptors for multistep attachment to target cells. The HS-GAG analog heparin decreased Ad5- and Ad2-mediated infection and binding starting from the concentration of 0.1 microgram/ml, up to a maximum of 50%. A similar reduction in Ad5 binding and infection was obtained by treatment of cells with heparin lyases I, II, and III but not with chondroitin ABC lyase. The effect of heparin on Ad5 binding has not been observed in surface GAG-defective Raji cells and after treating A549 cells with heparin lyases I, II,and III. The binding of Ad5 was completely abolished when both CAR was blocked with RmcB antibody and HS-GAGs were competitively inhibited by heparin. Parallel experiments demonstrate that HS-GAGs are irrelevant to binding and infection of the subgroup B adenovirus type 3. Collectively, these results demonstrate for the first time that HS-GAGs expressed on the cell surface are involved in the binding of Ad5 and Ad2 to host cells.

Evidence of mild respiratory disease in men with congenital absence of the vas deferens.

Cystic fibrosis (CF) is a severe disorder, whose main characteristics are, in addition to congenital absence of the vas deferens (CAVD), progressive lung disease, pancreatic insufficiency and elevated sweat chloride levels; CAVD without any other manifest clinical evidence is commonly suggested to be a form of CF with primarily genital expression. We undertook this study to test the hypothesis that men with a CAVD phenotype could be more CF-like than it is usually assumed. Each subject from a population of 42 patients suffering from CAVD was screened for a panel of 16 mutations plus the intron 8 5-thymidine allele of the CF gene (5T), and underwent a thorough clinical evaluation which included a detailed anamnesis, anthropometric data, chest and paranasal sinuses X-rays, pulmonary function tests, sputum cultures, stool chymotrypsin determination, sweat test and, in a limited number of patients, Nasal Potential Difference (NPD) measurement. The genotype analysis detected one compound heterozygote, 23 heterozygotes and 15 individuals carrying the 5T allele; sweat chloride was positive in six, borderline in 11 and negative in 25 subjects; NPD was abnormal in 2/12 patients. Medical history and clinical examination were consistent with respiratory disease in 20 cases; there was radiological evidence of pulmonary hyperinflation in 37/39 and of sinus disease in 20/42 patients; Staphylococcus aureus was cultivated in the sputum of 9/36, Haemophilus influentiae in 3/36 subjects and three patients showed functional evidence of airway obstruction. These findings were equally distributed among sweat positive, borderline and negative patients. These results raise questions about the supposed benignancy of the CAVD condition. A close follow-up of men with CAVD could ascertain potential complications.

Carrier testing program in a high-risk cystic fibrosis population from northeastern Italy. Active recruitment of relatives via probands' parents.

OBJECTIVE: To assess the practicability and monitor the results of an active carrier testing program among relatives of cystic fibrosis (CF) patients. METHODS: Parents of CF patients in the Veneto and Trentino regions of northeastern Italy were asked to help recruit relatives aged between 18 and 45 years for CF mutation testing. RESULTS: Of 409 enrolled CF parents, 59.6% agreed to send to the CF Center family composition data of relatives up to the third degree, and 28.8% recruited relatives to carrier testing, providing names and addresses of those who, being contacted, expressed a willingness to be tested. The participation of parents was higher if they were young and had a child recently diagnosed with CF. Recruiting parents indicated 333 close relatives (59%) for testing. When contacted by the CF Center, 170 of these 333 (51%) attended for testing. The percentage of close relatives who spontaneously asked for the test was 5.4% before the carrier testing program started; it rose to 25.3% following the introduction of the active strategy. CONCLUSIONS: The participation of the parents of CF patients is an important factor affecting the utilization of testing by relatives. Besides this, the influence of a favorable medical and cultural context (participation of gynecologists and family doctors in testing programs, genetic education of the general population) has to be considered.

Newborn screening strategy for cystic fibrosis: a field study in an area with high allelic heterogeneity.

To verify to what extent mutation analysis on blood spot could improve cystic fibrosis neonatal screening in an area with high allelic heterogeneity, we designed a special protocol. Spot trypsin estimation at birth, trypsin re-testing after 1 month, meconium lactase testing and mutation analysis of delta F508, R1162X and N1303K, were retrospectively clustered according to different patterns (trypsin/lactase/mutation; trypsin/lactase/re-testing; trypsin/mutation) and compared. The programme, which lasted 2 years (1993-94) and covered most of North-eastern Italy, included 95,553 screened newborns. Thirty-four affected babies were detected by screening and one by meconium ileus (incidence 1/2730). The combined use of trypsin, lactase and mutation analysis in cystic fibrosis neonatal screening permits a better sensitivity compared to the two other combinations (34 diagnoses vs 32 in both cases). Moreover, the higher specificity of the former method (false positives 42 vs 148) allows a reduction of recalls, which cause considerable anxiety. We confirm in trypsin-positive newborns an increased frequency of cystic fibrosis heterozygotes (1/17).

Nasal potential difference in cystic fibrosis patients presenting borderline sweat test.

The diagnosis of cystic fibrosis (CF) can be difficult if the sweat test and routine deoxyribonucleic acid (DNA) analysis are inconclusive. Under these circumstances, measurement of nasal potential difference (NPD) was proposed as a complementary diagnostic tool, as demonstrated in subjects bearing the G551S or 3849+10KbC-->T mutations. The purpose of the present study was to verify the diagnostic value of this technique in CF patients with a borderline sweat test. NPD was measured in 18 patients with a borderline sweat test, in whom CF diagnosis was based on the presence of one CF gene mutation in each chromosome (CF borderline). These patients were compared both to non-CF controls and CF patients with an abnormal sweat test (CF controls). Basal NPD values of CF borderline patients (mean value -39+/-6 mV, range -29 to -52 mV; n=18) were in the pathological range of CF controls (-39+/-8 mV, range -28 to -57 mV; n=37), and both were statistically different from values obtained in non-CF controls (-15+/-4 mV, range -6 to -23 mV; n=24; p<0.0001). Mutation analysis confirmed a high frequency of the 3849+10KbC-->T mutation in this group of CF borderline patients (positive in 14 out of 18 subjects), whereas other mutations, such as AF508, Q552X, N1303K and R1162X, were also found to be associated with this atypical CF phenotype. These results confirm the presence of pathological values of basal NPD in CF patients with borderline sweat test, and also extend this finding to subjects bearing genotypes other than the G551S and 3849+10KbC-->T mutations. The present findings, therefore, confirm the usefulness of measurement of basal nasal potential difference in all those patients in whom diagnosis of cystic fibrosis can be suspected but the sweat test remains inconclusive.

CFTR mutations and IVS8-5T variant in newborns with hypertrypsinaemia and normal sweat test.

Neonates positive for immunoreactive trypsinogen assay (IRT) and negative for sweat test have formerly been found to carry the major cystic fibrosis (CF) mutation, delta F508, much more frequently than the general population. Among the 716 IRT positive newborns detected by a three tier (IRT, mutation analysis plus meconium lactase assay, sweat test) CF screening programme in north eastern Italy during the period January 1993 to March 1996, we found 45 carriers, a number significantly higher than the expected 17 (p < 0.001). We speculated that some of these heterozygotes could actually be affected by a very mild form of CF, and carry on the other chromosome an undetected CFTR mutation or a DNA variant, such as the 5-thymidine allele in intron 8 of the CFTR gene (IVS8-5T). This hypothesis was tested in four samples; group A (the 45 carriers mentioned above), group B (51 non-carrier, IRT positive neonates), group C (50 IRT negative neonates), and group D (90 CF adult female carriers). Chromosomes with IVS8-5T were seven (7.78%) in group A, seven (6.86%) in group B, five (5%) in group C, and four in group D (2.22%). The 5T prevalence in group A was significantly higher (p < 0.05) compared to group D; similarly, a higher (p < 0.05) 5T frequency in group A compared to group C was detected by considering the chromosomes free from CFTR mutations. This study is consistent with previous papers in finding among neonates with high trypsin levels a CF carrier frequency significantly higher than that expected. It is also suggested that in at least some babies raised trypsin levels at birth could be a phenotypic expression of compound heterozygosity for a major CF mutation plus IVS8-5T.

Identification of a double mutation (D160V-K161E) in the p67phox gene of a chronic granulomatous disease patient.

In neutrophils of a chronic granulomatous disease (CGD) patient with a lack of p67phox the mRNA for p67phox was present in normal amount and size. This mRNA was reverse transcribed, and the coding region was analyzed by single-strand conformation polymorphism analysis. Direct DNA sequencing allowed the identification of a A479-to-T and A481-to-G substitution in exon 5 of the p67phox gene resulting in a double nonconservative amino acid change 160Lys-to-Glu and 161Asp-to-Val (D160V-K161E). This defect was found in the genomic DNA of this patient in heterozygous state and does not correspond to those previously found in other cases of CGD lacking the p67phox.

Analysis of the complete coding region of the CFTR gene in a cohort of CF patients from north-eastern Italy: identification of 90% of the mutations.

A complete coding-region analysis on 225 cystic fibrosis (CF) chromosomes from a cohort that includes all the affected subjects born in two North-Eastern Italian regions over eight years was performed. In a previous study, we identified mutations on 166/225 (73.8%) CF chromosomes after screening for 62 mutations. To characterise the remaining 59 CF chromosomes, we carried out automated direct DNA sequencing (exons 9 and 13), RNA single-strand conformation polymorphism (exons 1-8 and 10-12) and denaturing gradient gel electrophoresis (exons 14a-24) of the 27 exons and flanking regions of the CF transmembrane conductance regulator gene. We identified 22 mutations, four of which are novel, viz. 711 + 5G-->A, R709X, 3132delTG and 2790-2A-->G, and we characterised 90.2% (203/225) of the CF chromosomes. Taking advantage of the homogeneity of the sample, an evaluation of the most important clinical parameters, assessed at the age of 12 years, is presented. We confirm some previously reported genotype-phenotype correlations and we report a new nonsense mutation (R709X) associated with a pancreatic sufficient phenotype.

Cystic fibrosis: the delta F508 mutation does not lead to an exceptionally severe phenotype. A cohort study.

In an attempt to ascertain a relationship between genotype and phenotype, we studied the pulmonary and nutritional status of 123 cystic fibrosis patients with known genotype at an age of 8.5-10 years. Patients represent a cohort as they are almost all those born and diagnosed in a given area and period. They were followed at a single centre using uniform diagnostic and treatment protocols. Pulmonary and nutritional status of homozygous delta 508 patients did not differ from that of compound heterozygotes or of patients with other unspecified genotypes. Pulmonary manifestations varied widely in all genotype groups. With the given number of patients, a slightly higher mortality of delta F508 homozygotes could have been coincidental. We conclude that up to the age of 8.5-10 years the severity of pulmonary lesions and nutritional deficiencies is not related to the delta F508 mutation.