Recently there has been an explosive increase in molecular diagnostics. This is due to translational research on the molecular basis of human diseases, and to technological developments that have resulted in efficient procedures for extensive analysis of the human genome. However, a large body of data on the genome is still difficult to interpret at the clinical level. For many monogenic diseases, “modifier” genes, inherited independently of the disease gene interact, thereby resulting in a distinct phenotype for each patient. Multigenic diseases depend on complex interactions between genes and the environment. Response to drugs and side effects are modulated by gene variants. The same is true for the response to nutrients. All these interactions, which vary from patient to patient, led to the concept of “personalized medicine”. Our genome consists of 25,000 genes, a surprisingly low number when compared to other species. Therefore, the complex phenotype of humans depends on a number of mechanisms that regulate gene expression, which, in turn, may be altered resulting in disease. For example, DNA methylation modulates the level of gene expression, and altered methylation of some genes is related to human neoplasias. MicroRNAs regulate the expression of a myriad of genes, and mounting evidence indicates that this mechanism may be impaired in human diseases. Finally, the relationships between genetics and human behavior are starting to be elucidated. For example, suicide may be related to alterations of methylation of specific genes. To conclude: the chip-wide analysis of human genomes is becoming easier, but the understanding of molecular genetics that confirmed the real “uniqueness” of each genome is an excellent opportunity for laboratory medicine to reposition the patient at the heart of the medical process.
We compared the analytical accuracy, times, costs and
the detection rate of four procedures for the molecular
analysis of cystic fibrosis (CF).
DNA from 127 subjects bearing different genotypes
was tested by denaturating gradient gel electrophoresis
followed by sequencing (reference procedure) and,
for comparison, by ASO dot-blot (in-house), reverse
dot-blot (Innogenetics), ARMS (Zeneca Diagnostics)
and OLA-PCR (PE Applied Biosystem). To assess inter-observer
variability, all samples were tested twice. To
evaluate intra- and between-series variability, two
samples were tested twice in each series.
All the procedures yielded reproducible results and
assigned the correct genotype to each sample. ASO
dot-blot is the cheapest procedure but has the longest
analytical time (>24 h) and uses radioactive labeling. It
can be adapted to analyze peculiar mutations in specific
ethnic groups. ARMS from Zeneca Diagnostics is
rapid (4 h), easy to perform, but, except for the
∆F508 mutation, does not distinguish the homozygote
from the heterozygote genotype. It could be used for
carrier analysis in families with known mutations.
OLA-PCR has the highest detection rate in most ethnic
groups, is automated for capillary electrophoresis but
requires a high level of operator expertise: it is suitable
when collected series of samples are analyzed from
large patient cohorts. Reverse dot-blot is easy to perform
and can be semiautomated: it can be used as
first-line screening test. Given the heterogeneity of CF
mutations, commercial kits should be developed to
analyze mutations peculiar to specific ethnic groups.
Background: The demand for molecular prenatal diagnosis (PD) of inherited diseases to help high-risk couples make informed reproductive decisions has increased in the past decade.
Methods: We provided multidisciplinary pre-test counselling to 1248 couples at high risk of having a child affected by an inherited disease.
Results: After multidisciplinary counselling, 1171 couples requested PD for one of 73 inherited diseases. Of these, 995 (85.0%) were performed on DNA from chorionic villi (CV) and 176 (15.0%) on samples from amniocentesis. The occurrence of pregnancy loss (0.6%) and major complications did not differ significantly between the two groups. We made a diagnosis in all cases (including 8 twin pregnancies) except in 4/995 cases of CV sampling (0.4%) and in 3/176 of amniocentesis (1.7%) due to insufficient DNA. In 15 cases, molecular analysis revealed non-paternity.
Conclusions: PD by analysis of foetal DNA from CV is a reliable aid in reproduction decision-making for couples at high risk of inherited diseases. The complexity of experimental procedures and the specific expertise required for the pre- and post-test multidisciplinary counselling suggest that PD be performed in reference centres also within the framework of supranational networks.
Background: The demand for prenatal diagnosis (PD) of cystic fibrosis (CF) is increasing.
Methods: We performed pre-test multidisciplinary counselling for 192 couples at CF reproductive risk. In 11/192 (5.7%) cases PD was not performed mainly because counselling revealed a reproductive risk for atypical (mild) CF, while 181 PDs were performed in couples revealed at high risk for CF mainly because they already had a CF child (148/181, 81.8%) or had been identified through cascade screening (28/181, 15.5%).
Results: In 167/181 (92.3%) cases (including two dichorionic twin pregnancies), PD was performed on chorionic villi, and in 14 on amniocyte DNA. Only 1/181 PD was unsuccessful. In all other cases, single tandem repeat analysis excluded maternal contamination, and PD was made within 7 days of sampling. In total 116/180 (64.4%) PDs were made with dot-blot analysis; 40 (22.2%) required gene sequencing; in 4/180 cases we tested the gene for large rearrangements; in 23/180 (12.8%) cases linkage analysis was necessary because parental mutation(s) were unknown. Forty-two out of 180 (23.3%) PDs revealed an affected foetus. All couples but one interrupted pregnancy. The first twin PD revealed the absence (1 foetus) and the presence of one mutation (the other foetus); the second twin PD revealed one parental mutation (1 foetus) and both parental mutations (the other foetus); the couple planned selective interruption.
Conclusions: PD for CF should be performed in reference laboratories equipped for gene scanning and linkage analysis, with a multidisciplinary staff able to offer counselling to couples during all phases of PD.
Background: Human β-defensins (hBDs) are small cationic, widely expressed proteins involved in innate immunity that exert strong bactericidal activity toward various pathogens. However, the role of hBDs in various diseases to which bacterial infection add severity, as it is in celiac disease (CD), is not yet clear. We analyzed the expression of the hBD1, hBD2, hBD3 and hBD4 genes in patients with CD during the active phase and after remission following a gluten-free diet to determine their role in development and relapse of CD.
Methods: We studied 21 unrelated adults with CD (confirmed by anti-thyroglobulin antibodies and intestinal biopsy); 14 were evaluated at diagnosis, before diet modification, and seven after 2 years of a gluten-free diet. Thirty-six unrelated adults served as controls. We analyzed the mRNA expression of hBD1, 2, 3 and 4 on biopsy samples of duodenum obtained from all patients during endoscopy for diagnostic purposes. We used real-time polymerase chain reaction with TaqMan probes and obtained gene expression data using the delta-Ct method.
Results: hBD1 mRNA was significantly lower in patients with active CD compared with patients on diet modification, whereas the mRNA levels of the other three defensins did not differ significantly between the two subgroups. Interestingly, the gluten-free diet restored only partially hBD1 expression as compared to a normal group of celiac-free subjects.
Conclusions: Our data reinforce the evidence that hBD1 expression is greatly reduced in the duodenum of patients with active CD. It also strengthens the concept that reduced activity of immune peptides may predispose individuals to bacterial proliferation that contributes to the pathogenesis of CD.
Background: Haemophilia A and B (HA, HB) are the most frequent X-linked bleeding diseases; two-thirds of cases are severe.
Methods: We counselled 51 couples for prenatal diagnosis (PD) of haemophilia. In 7/51 (13.7%) cases, the couple decided not to undergo PD because counselling revealed that they were carriers of a mild form of the disease, while we performed 44 PD for severe HA (36 cases) or HB (8 cases). The indication for PD was a haemophilic child (30/44, 68.2%) or an affected family member (12/44, 27.3%); in two cases the non-carrier mother of isolated haemophilic patients requested PD because of the risk of mosaicism.
Results: We completed PD in 43/44 cases; in one case, the prenatal sample was contaminated by maternal DNA; however, molecular analysis revealed the female sex of the foetus. We performed PD for 16 of the 36 couples at risk of HA (44.4%) by analysing the intron (IVS)22 inversion; in 1/36 cases (2.8%) the mother had the IVS1 inversion, and in 8/36 (22.2%) the family mutation was identified by sequencing; in 11/36 (30.6%) cases the family mutation was unknown, and PD was performed by linkage (no recombination nor uninformative cases occurred). For HB, in 6/8 (75.0%) cases, PD was performed by DHPLC or by sequencing; in 2/8 cases we tested intragenic markers (again with no cases of recombination or uninformative families).
Conclusions: PD in well-equipped laboratories, and multidisciplinary counselling are an aid to planning reproductive and early therapeutic strategies in families with severe haemophilia.
Haemophilia A is the most common inherited bleeding disorder caused by defects in the F8C gene that encodes coagulation factor VIII. This X-linked recessive disorder occurs in approximately 1:5000 males. Haemophilia A is diagnosed based on normal prothrombin time, altered activated partial thromboplastin time and reduced factor VIII activity in plasma. Carrier females are usually asymptomatic and can be identified only by molecular analysis. The most frequent mutations in F8C are intron 22 and 1 inversions, which occur in approximately 50% and 5% of patients, respectively, with a severe phenotype. Large gene deletions are observed in approximately 5% of alleles from patients with severe haemophilia A. The remaining severe cases and all moderate and mild cases result from numerous point mutations and small insertions/deletions, which are de novo mutations in one-third of cases. Thus, molecular diagnosis of carrier status and prenatal diagnosis in families without intron 22 or 1 inversions is based on scanning techniques or gene sequencing. When the disease-causing mutation cannot be identified, molecular diagnosis is performed by linkage analysis of several DNA polymorphic markers linked to F8C. Given the clinical heterogeneity among haemophilic patients, many groups, including our own, have examined the relationships between prothrombotic gene variants and haemophilic phenotype to investigate whether prothrombotic gene variants modify clinical expression of the disease.
Thanks to its typical expression, haemophilia can be identified in writings from the second century AD. Haemophilia B, an X-linked recessive bleeding disorder due to factor IX (FIX) deficiency, has an incidence of about 1:30000 live male births. The factor 9 (F9) gene was mapped in 1984 on Xq27.1. Haemophilia is diagnosed from prothrombin time, activated partial thromboplastin time, and FIX levels. Carrier females are usually asymptomatic and must be identified only with molecular analysis. Linkage analysis of F9 polymorphisms is rapid and inexpensive but limited by non-informative families, recombinant events, and the high incidence of germline mutations; thus, various procedures have been used for the direct scan of F9 mutations. We set up a novel denaturing high performance liquid chromatographic procedure to scan the F9 gene. This rapid, reproducible procedure detected F9 mutations in 100% of a preliminary cohort of 18 haemophilia B patients. Parallel to the development of more efficient diagnostic tools, the life expectancy and reproductive fitness of haemophilic patients have greatly improved and will continue to improve thanks to the use of less immunogenic recombinant FIX. Hopefully, new approaches based on gene therapy now being evaluated in clinical trials will revolutionise haemophilia B treatment.
Low cholesterol is typically observed in the plasma of patients with cystic fibrosis (CF) contrasting with the subcellular accumulation of cholesterol demonstrated in CF cells and in mice models. However, the homeostasis of cholesterol has not been well investigated in patients with CF.
We studied the plasma of 26 patients with CF and 33 unaffected controls campesterol and β-sitosterol as markers of intestinal absorption and lathosterol as a marker of de novo cholesterol biosynthesis by gas chromatography (GC-FID and GC-MS).
Plasma campesterol and β-sitosterol results were significantly (p=0.01) lower while plasma lathosterol was significantly higher (p=0.001) in patients with CF as compared to control subjects. Plasma cholesterol results were significantly lower (p=0.01) in CF patients.
Our data suggest that the impaired intestinal absorption of exogenous sterols in patients with CF stimulates the endogenous synthesis of cholesterol, but the levels of total cholesterol in plasma remain lower. This may be due to the CFTR dysfunction that reduces cholesterol blood excretion causing the accumulation of cholesterol in liver cells and in other tissues contributing to trigger CF chronic inflammation.