A 343 Italian cohort of patients analysed with array-comparative genomic hybridization: unsolved problems and genetic counselling difficulties.

BACKGROUND: The recent introduction of microarrays for genetic analyses has allowed higher etiological diagnostic rates in patient with intellectual disability (ID), autism spectrum disorders (ASD), epilepsy and multiple congenital anomalies (MCA), because of its resolution. This approach still results of high complexity and some limitations have been reported. In fact, it discloses several variants of unknown significance (VOUS) or incidental findings. In all cases, a massive amount of data is generated, because of this, the analysis and the interpretation is very difficult and often without a definitive conclusion. METHOD: We analysed an Italian cohort of 343 patients with ID, MCA and ASD by array-comparative genomic hybridization. The purpose of this work was to consider the proportion of the chromosomal abnormalities in such cohort and to assess the distribution of the different type of the chromosomal abnormalities concerning their pathogenic significance, their origin and their correlation to these clinical phenotypes. RESULTS: Array-comparative genomic hybridization analysis revealed 76 positive results. Abnormalities were detected in 27.8% of patients with ID, 11.1% with ASD, 10.7% with epilepsy and 19.4% with multiple congenital anomalies. The anomalies were classified in three major groups: group 1 (27 patients) with pathogenic alterations (P group); group 2 (34 patients) with VOUS potentially pathogenic (PP group); and group 3 (13 patients) with VOUS potentially benign (PB group). As expected, comparing the diagnostic groups, we observed a greater number of deletions in the P group and that all the abnormalities of the PB group were inherited. CONCLUSIONS: Our retrospective study resulted in confirming the high detection rate of microarrays. CNV classification remains a complex procedure. The difficulty in CNV classification points out the importance of the patient selection, helping the interpretation of the molecular cytogenetic results.

A new case of pure partial 7q duplication.

We report on an 18-month-old boy conceived by assisted reproduction technology with developmental delay, hypotonia, microcephaly, frontal bossing, a mild convergent squint, malformed ears, and a short neck. Karyotype analysis revealed a de novo 7q21.1q22.3 duplication characterized by array comparative genomic hybridization (array-CGH) as a segment of 18.69 Mb. Duplications of the long arm of chromosome 7 are uncommon. There are 18 reported cases of different 7q segments with a pure duplication with no additional deletion of other chromosomes. As a consequence, duplications of chromosome 7q have been classified in 4 groups on the basis of the involved region. The present case is included in group 3 which involves interstitial duplications of different sizes. In the literature, only one case with an apparently smaller duplication of the same region has been described. Despite this, the phenotype is different. Moreover, the 2 patients share some phenotypic features, such as psychomotor delay, hypotonia, frontal bossing, short neck, and strabismus. However, the absence of physical characterization in most of the reported cases could justify the lacking phenotype-genotype correlation in patients with partial 7q duplication. Further studies using recent molecular approaches such as array-CGH might permit a more clinically useful grouping of 7q duplications.

Inositide-specific phospholipase c beta1 gene deletion in the progression of myelodysplastic syndrome to acute myeloid leukemia.

Myelodysplastic syndrome (MDS) is an adult hematological disease that evolves into acute myeloid leukemia (AML) in about 30% of the cases. The availability of a highly specific probe moved us to perform in patients affected with MDS/AML, associated with normal karyotype, painting and fluorescence in situ hybridization (FISH) analysis aimed to check the inositide-specific phospholipase C (PI-PLC) beta1 gene, a player in the control of some checkpoints of the cell cycle. Here we present a preliminary observation in which FISH analysis disclosed in a small group of MDS/AML patients with normal karyotype the monoallelic deletion of the PI-PLCbeta1 gene. On the contrary, PI-PLC beta4, another gene coding for a signaling molecule, located on 20p12.3 at a distance as far as less than 1Mb from PI-PLCbeta1, is unaffected in MDS patients with the deletion of PI-PLC beta1 gene, hinting at an interstitial deletion. The MDS patients, bearing the deletion, rapidly evolved to AML. The data suggest the possible involvement of PI-PLCbeta1 in the progression of the disease and pave the way for a larger investigation aimed at identifying a possible high-risk group among MDS patients with a normal karyotype.

Deletion of the SHOX gene in patients with short stature of unknown cause.

A fluorescence in situ hybridization (FISH) study was performed in 56 patients with short stature of unknown cause in order to establish the role of deletion of the SHOX gene in this population. FISH analysis was carried out on metaphase spreads and interphase lymphocytes from blood smears using a probe specific for the SHOX gene. Deletion of SHOX was found in four patients (7.1%). No skeletal abnormalities were detected in these patients either at the physical examination or at X-rays of the upper and lower limbs. Present results indicate that SHOX plays an important role also in short stature of unknown cause, and FISH analysis appears as an easy, appropriate, and inexpensive method for the detection of SHOX deletion.

Genomic organization, physical mapping, and involvement in Yq microdeletions of the VCY2 (BPY 2) gene.

VCY2 is a gene positioned within the AZFc locus of the Y chromosome, a region frequently deleted in infertile males. To investigate the involvement of this gene in idiopathic male infertility, we studied its genomic organization and localization. Analysis of the genomic structure demonstrated that the VCY2 gene is composed of 9 exons spanning 21 kb. FISH analysis on interphase nuclei with specific probes for exons 4-6, 7, and 8 demonstrated the presence of a single gene copy, and Fiber-FISH on relaxed chromatin indicated that VCY2 is located within the DAZ gene cluster. PCR, Southern blot, and FISH analysis on infertile patients with Yq microdeletions demonstrated the absence of VCY2 in all cases where deletions involved the DAZ gene, raising the question about the role of the VCY2 gene loss in the phenotype reported for DAZ-deleted patients.

Spectral karyotyping (SKY) refinement of a complex karyotype with t(20;21) in a Ph-positive CML patient submitted to peripheral blood stem cell transplantation.

A patient with a Ph-positive chronic myeloid leukaemia (CML) was submitted to allogeneic peripheral blood stem cell transplantation from an HLA-haploidentical related donor 7 years after the diagnosis. Six months later, he showed a disease relapse while cytogenetic analysis displayed a complex karyotype. To characterise the chromosomal rearrangements spectral karyotype (SKY) analysis was used. This redefined all chromosome rearrangements and revealed a t(20;21)(q11;q22). FISH analysis with a specific probe for the AML1 gene disclosed disruption of this gene which was partially translocated on to the long arm of chromosome 20. It is likely that this rearrangement, unusual for CML, was implicated in the disease evolution towards blastic crisis (BC).

Characterization of novel genes in AZF regions.

The long arm of the Y chromosome contains genes mapped in loci involved in male infertility, short stature and gonadoblastoma. However, many of these genes have not been fully characterized, and are not currently investigated in patients affected by such diseases. We report a study aimed to the genomic characterization of 5 genes mapped within the Y chromosome: BPY2, PRY, TTY1, TTY2, and VCY. Exon-intron boundaries were detected for each gene, and PCR analysis was carried out to investigate the involvement of these genes in different re-arrangements of the Y chromosome. It was found that BPY2 and PRY are lost in some infertile patients with Yq microdeletions, suggesting that they could play a role in male gametogenesis. On the other hand, these patients retain some copies of TTYI and TTY2 genes, due to the presence of copies in Yp, and of VCY, which has homologous copies on the X chromosome. On the basis of their localization, these genes could be candidate for the gonadoblastoma locus (TTY1, TTY2) and for the control growth locus (VCY).

Narrowing the Duane syndrome critical region at chromosome 8q13 down to 40 kb.

Duane syndrome (MIM 126800) is an autosomal dominant disorder characterised by primary strabismus and other ocular anomalies, associated with variable deficiency of binocular sight. We have recently identified a < 3 cM smallest region of deletion overlap (SRO) by comparing interstitial deletions at band 8q13 in two patients (one described by Vincent et al, 1994, and the other by Calabrese et al, 1998). Here we report on another patient with Duane syndrome carrying a reciprocal translation t(6;8)(q26;q13). FISH and PCR analyses using a YAC contig spanning the SRO narrowed the Duane region to a < 1 cM interval between markers SHGC37325 and W14901. In addition, the identification and mapping of two PAC clones flanking the translocation breakpoint, allowed us to further narrow the critical region to about 40 kb. As part of these mapping studies, we have also refined the map position of AMYB, a putative candidate gene, to 8q13, centromeric to Duane locus. AMYB is expressed in brain cortex and genital crests and has been previously mapped to 8q22.

FISH analysis in detecting 9p duplication (p22p24).

Authors report on a case of partial 9p duplication, involving the 9p22-9p24 region. This represents the second case of such duplication in which the breakpoints were precisely defined using fluorescence in situ hybridisation (FISH) with chromosome 9 specific painting and YAC DNA probes, localised onto 9p22-9p24 region. FISH analysis pinpointed chromosome breakpoints in dup(9)(p22p24) and excluded an insertion or a translocation from other chromosomes. The present report supports the segment 9p22-9p24 as the critical region for the observed phenotype of the duplication 9p syndrome.

Loss of the SHOX gene associated with Leri-Weill dyschondrosteosis in a 45,X male.

A male patient is reported with a 45,X karyotype and Leri-Weill dyschondrosteosis (LWD). FISH analysis with SHOX and SRY gene probes was carried out. One copy of both SHOX and SRY was detected in interphase nuclei, clarifying the origin of LWD and the male phenotype. Molecular results suggested that the 45,X karyotype arose through two independent events. The first occurred at paternal meiosis leading to an unequal crossing over between the short arms of the X and Y chromosomes. As a consequence, the SRY gene was translocated onto Xp, thereby explaining the male phenotype of the patient. The second event probably occurred at maternal meiosis or at the early stages of the zygote resulting in the loss of the maternal X chromosome.

Prenatal diagnosis using the triple test.

METHODS: A screening study performed on 2,803 pregnant women using the "triple test" is reported. RESULTS: Nine hundred and twenty-one had a high prior risk, having > 35 years while, after the screening, only 201 women had a positive test at risk higher than 1:270, and underwent to amniocentesis. The detection rate (DR) for all abnormalities was 91% while for Down's syndrome (DS) it was 87.5% and for neural tube defects 85.5%. Foetal abnormalities were detected in 20 cases (1:10) while 181 were false positive cases (6.5%), of which 151 for DS (5.4%). False negative were observed only in 2 cases within 2,339 at term pregnancies. CONCLUSIONS: The authors retain that high DR is related to the exactness of determination of gestation age calculated by scan and to the homogeneity of the examined population.

Detection of an insertion deletion of region 8q13-q21.2 in a patient with Duane syndrome: implications for mapping and cloning a Duane gene.

Duane syndrome (MIM126800) is an autosomal dominant disease responsible for 1% of all strabismus cases and has been related to a 8q12-13 contiguous gene syndrome. We report on an insertion of chromosome region 8q13-q21.2 on to band 6q25 in a patient presenting with Duane syndrome, mental retardation, and other dysmorphisms. FISH analysis using chromosome 8 radiation hybrid LIA2L indicated a concurrent deletion within the 8q rearranged region. These results were corroborated by STR-PCR analysis and FISH using YAC contig WC8.8 disclosed a deletion in 8q13. Comparison of the two known patients with Duane syndrome associated with deletion of 8q identifies a small region of overlap (SRO) of < 3 cM extending from D8S533 and D8S1767 in which a Duane syndrome locus is assigned. In addition YAC analysis in our patient showed that 8q rearrangement was rather complex since 8q deletion and insertion occurred in two distinct segments separated by a region which maintained its location on 8q.

A quarter of men with idiopathic oligo-azoospermia display chromosomal abnormalities and microdeletions of different types in interval 6 of Yq11.

Cytogenetic investigations and molecular analysis of the Y chromosome by the polymerase chain reaction amplification of sequence-tagged sites (STS-PCR) technique were performed in 126 patients affected by idiopathic oligo-azoospermia following accurate selection of cases. Seventeen patients evidenced an abnormal karyotype. Fourteen patients with a normal karyotype had microdeletions of the Y chromosome within interval 6. In azoospermic patients microdeletions were scattered along different subintervals, while in oligozoospermic patients they were clustered in subinterval 6E. The size of the deletion was not apparently related to the severity of the disease. These results suggest that cytogenetic analysis and the STS-PCR technique can detect a genetic cause of infertility in about one-quarter of patients with idiopathic oligo-azoospermia.

Comparative Study of FISH, PCR and Cytogenetics on 25 Patients Submitted to Bone Marrow Transplantation (BMT) for Chronic Myelogenous Leukemia (CML); Which Tests can we Use in Routine Analysis Post BMT?

Chronic Myeloid Leukaemia (CML) shows an excellent response to allogeneic bone marrow transplantation (BMT) with a 60-80% long term disease free survival in recipients of unmanipulate marrow. The most frequent cause of treatment failure is leukaemic relapse, due to the re-emergence of malignant recipient clones. Clinical and haematological relapse is usually preceded by molecular evidence of relapse. Early detection of molecular relapse may allow intervention with immunotherapy such as donor lymphocyte infusions (DLI). This study was undertaken to compare results from two centres who employ either Fluorescent In Situ Hybridisation (FISH) or polymerase chain reaction (PCR) analysis of DNA polymorphisms as their routine method of detecting residual host cells following BMT for CML in order to establish (1) if these methods are equivalent for routine laboratory use in reporting of chimaerism results to the referring clinician, and (2) if these methods are beneficial for indicating new and early therapeutic strategies. FISH analyses for the X and Y chromosomes (in sex mismatched patients) and/or FISH for BCR and ABL loci were compared with short tandem repeat PCR (STR-PCR) and conventional karyotyping in serial analyses in 25 patients submitted to BMT for Philadelphia positive (Ph) CML. Comparison of all results on samples assessed between 1 and 13 years post BMT indicated that FISH and PCR, performed on the same bone marrow samples displayed similar results in more than 90% of patients in first 3 years after BMT which increased to a concordance rate of 100% in long term survivors. In contrast, comparison of FISH or PCR versus cytogenetic analysis indicated a low concordance rate, with less than 50% of samples showing similar results during all the follow-up period. Eighty percent of recipients (22 patients) had evidence of mixed chimaerism following BMT (initial level of positivity 1-6% recipient cells) during the follow-up period. This low percentage of recipient cells remained stable in 7 patients, while 9 patients reverted to a donor profile. All 16 patients are in haematological remission. In addition the 3 patients with complete donor chimaerism remain in remission. In the remaining 6 patients, a progressive increase in recipient cells occurred (progressive mixed chimaerism, PMC), and was followed by haematological relapse. We conclude that FISH and PCR can be used to monitor CML patients post BMT and transient or stable low level mixed chimaerism is not associated with leukaemia relapse, but PMC is predictive of imminent relapse and its detection may help to illucidate the timing of early intervention with donor lymphocyte infusion.

Clustering of Y chromosome deletions in subinterval E of interval 6 supports the existence of an oligozoospermia critical region outside the DAZ gene.

Y chromosome molecular analysis was performed using the STS-PCR technique in 50 patients with oligozoospermia. Microdeletions of interval 6 of the Y chromosome were detected in seven patients, in six of whom subinterval E was affected. All patients retained the RBM1 and DAZ genes, while in one deletion involved the SPGY gene. The size of the deletion was not apparently related to the severity of the disease. These results suggest the presence of an oligozoospermia critical region on the Y chromosome within subinterval E of interval 6.