PCR Of Short Fluorescent Fragments Research Articles

Frontotemporal Dementia Phenotype Associated with MAPT Gene Duplication

Microduplications at 17q21.31 have recently been reported in children with mental retardation, autism spectrum disorders and/or dysmorphic features, as well as in a single schizophrenic patient. This rearrangement encompasses the microtubule associated protein tau (MAPT) gene, mutations of which are a major cause of frontotemporal lobar degeneration (FTLD). However, no 17q21.31 microduplication has been so far identified in this condition. We screened chromosomal rearrangements in FTLD patients using quantitative multiplex PCR of short fluorescent fragments and high resolution array CGH. We found a 439-kb microduplication at the 17q21.31 locus encompassing the MAPT, IMP5, CRHR1, and STH genes in the index case of a family in which three patients have developed a FTLD phenotype associated with marked memory impairment. None of these patients had mental retardation or dysmorphic features. Since no pathological examination was available, we are not certain that this case corresponds to a FTLD with neuronal and glial tau inclusions (FTLD-tau), and we cannot exclude that any other gene included in the rearrangement might be responsible for the neurodegenerative process. However, the clinical phenotype of the three patients is functionally consistent with the regional pattern of lesions previously reported in mice overexpressing human tau.

The Succinate Dehydrogenase Genetic Testing in a Large Prospective Series of Patients with Paragangliomas

Germline mutations in SDHx genes cause hereditary paraganglioma. The aim of the study was to assess the indications for succinate dehydrogenase (SDH) genetic testing in a prospective study. A total of 445 patients with head and neck and/or thoracic-abdominal or pelvic paragangliomas were recruited over 5 yr in 20 referral centers. In addition to classical direct sequencing of the SDHB, SDHC, and SDHD genes, two methods for detecting large genomic deletions or duplications were used, quantitative multiplex PCR of short fluorescent fragments (QMPSF) and multiplex ligation-dependent probe amplification (MLPA). A large variety of SDH germline mutations were found by direct sequencing in 220 patients and by QMPSF and MLPA in 22 patients (9.1%): 130 in SDHD, 96 in SDHB, and 16 in SDHC. Mutation carriers were younger and more frequently had multiple or malignant paraganglioma than patients without mutations. A head and neck paraganglioma was present in 97.7% of the SDHD and 87.5% of the SDHC mutation carriers, but in only 42.7% of the SDHB carriers. A thoracic-abdominal or pelvic location was present in 63.5% of the SDHB, 16.1% of the SDHD, and in 12.5% of the SDHC mutation carriers. Multiple paragangliomas were diagnosed in 66.9% of the SDHD mutation carriers. A malignant paraganglioma was documented in 37.5% of the SDHB, 3.1% of the SDHD, and none of the SDHC mutation carriers. SDH genetic testing, including tests for large genomic deletions, is indicated in all patients with head and neck and/or thoracic-abdominal or pelvic paraganglioma and can be targeted according to clinical criteria.

INTRAFAMILIAL DIVERSITY OF PHENOTYPE ASSOCIATED WITH APP DUPLICATION

Different APP locus duplications have been recently identified in rare families with autosomal dominant early onset Alzheimer disease (AD) and Aβ-related cerebral amyloid angiopathy (CAA).1–3 We report a novel family revealing a very large diversity of phenotype including dementia with Lewy bodies (DLB). ### Methods. Family members gave informed consent according to a protocol approved by the ethics committees of the CCPPRB Pitie-Salpetriere and Paris-Necker. Characterization of five patients, with two detailed neuropsychological evaluations, brain MRI of three patients, and one neuropathologic evaluation, were assessed. APP locus was analyzed by quantitative multiplex PCR of short fluorescent fragments (QMPSF) in three patients. Patients were considered affected if they had dementia, intracerebral hemorrhage (ICH), or epilepsy (e-Methods on the Neurology ® Web site at www.neurology.org). ### Results. The proband (II-1, figure e-1) developed bradykinesia, memory problems, and apraxia when she was 44 years old. She developed paranoid delusion with visual hallucinations at 50 years of age. The association with bilateral tremor, rigidity, and bradykinesia was suggestive of DLB. Several T2 lesions were noted on MRI. She died at 55 years of age. Patients I-2 and I-3 had progressive memory disturbances with behavioral changes suggestive of AD since they were 55 and 60 years of age. Patient II-3 had partial visual seizures at the age …

Gene Expression Profile Analysis According to Recurrent Gene Copy Number Abnormalities Defines a Diffuse Large B-Cell Lymphoma Subgroup Characterized by 9p21 Locus Deletion, Ribosome Machinery Deregulation and Poor Prognosis. A GELA Study

Genomic gains and losses play a crucial role in the development and progression of DLBCL. Some gains or losses are associated with particular morphologic or clinical manifestations and correlate with the “germinal center B-cell like” (GCB)/non-GCB phenotype, as defined by gene expression profiles (GEP). We previously developed a reliable and routinely single applicable PCR assay, which provided information regarding gain/loss of relevant genes, and prognosis in DLBCL, termed QMPSF (Multiplex PCR of Short Fluorescent Fragments). Here, we combined GEP and QMPSF approaches to delineate molecular pathways related to recurrent gene copy number abnormalities (GCNA) and assess their prognosis value in patients treated by R-CHOP. For this purpose a series of 69 newly diagnosed DLBCL, included in the 98–5 GELA trial with available tumor DNA was studied (median age = 69 years [59–79], IPI2–3: 64%; 4–5: 36%, 40 treated by R-CHOP and 29 by CHOP). A single QMPSF assay, validated by CGH array, to detect GCNA of 8 relevant genes including SIM1 (6q16), MYC (8q24), CDNK2A (9p21), RB1 (13q14), REL (2p13), BCL2 (18q21), TP53 (17p13), and CDKN1B (12p13) was performed. In addition a dedicated QMPSF assay that provides a “bar code” of the 9p21 locus containing CDKN2A (p16INK4a and p14ARF) and CDKN2B (p15INK4b) was designed. To delineate specific gene expression profile according to recurrent GCNA a subset of 52 patients were studied by both GEP (Affymetrix U133A) and QMPSF technologies. Gains of MYC, BCL2, and REL were observed in 13, 28 and 20 % respectively. DNA copy losses of TP53, CDNK2A, RB1 and SIM1 were observed in 9, 40, 6 and 17 % of cases respectively. Using supervised analysis, we delineated specific GEP according to the most frequent GCNA detected by QMPSF. Interestingly, a signature related to 9p21 locus (CDKN2A/CDKN2B) deletion was associated with an overexpression of several ribosome machinery coding genes and the involvement of distinct antiapoptotic molecular mechanisms. Subsequent genomic analysis with the dedicated assay indicated that in most of cases deletions were homozygous and abolished simultaneously p14arf and p16INK4a expression. With a median follow-up of 81 months, CDKN2A deletion, strongly correlates to a poor outcome in the entire cohort (5y OS=25% respectively vs.60% for patients in germline configuration, p=.003) and in the subgroup of patients treated by R-CHOP (5y OS=40% vs.70%, p=.04). Furthermore, prognosis impact of GCNA involving CDKN2A was validated in an independent set of 35 patients treated by R-CHOP. To conclude, combination of QMPSF and GEP may constitute a powerful approach to delineate new genomic pathways with prognosis impact in DLBCL. Notably, CDKN2A/CDKN2B loss, detected in more than one third of DLBCL patients constitutes a strong factor of chemoresistance that is not overcome by R combination. GEP indicates that this may be a consequence of an independent p14arf/p53 pathway, involving the well-established p14arf related ribosome regulation function.

Incidence and Clinicopathological Relevance of Gene Copy Number Abnormalities Detected by a Single Quantitative PCR Assay in Mantle Cell Lymphomas.

The genetic hallmark of mantle cell lymphoma (MCL) is the t(11;14)(q13;q32). Fluorescence in situ hybridisation (FISH) and microarray based comparative genomic hybridisation (array CGH) experiments have demonstrated that additional genetic clonal alterations occur in the majority of MCL and may have prognostic or pathological relevance. We previously developed and validated by CGH or FISH an inexpensive and sensitive genomic PCR assay (Multiplex PCR of Short Fluorescent Fragments, QMPSF) to detect gene copy number abnormalities in diffuse large B-cell lymphoma and chronic lymphocytic leukemia (Haematologica 2008,93:543-Leukemia, 2007,21:1460). In the aim to determine the incidence and clinical relevance of recurrent additional genomic number abnormalities, we specifically designed a single QMPSF assay dedicated for MCL and correlated results with pathological and clinical data. For this purpose, a series of 42 newly diagnosed MCL cases with available frozen-and paraffin-embedded lymph node tissues and clinical features were selected [median age=67y; median MCL international prognostic index (MIPI)=6.1; low risk 21%, intermediate risk 33%, high risk 45%; 3-year overall survival (OS) rate=38%]. The assay was designed according to the most frequent gene copy number abnormalities reported in MCL, allowing simultaneous analysis of 8 relevant genes (CDKN2A, RB1, ATM, CDK2, TP53, MYC, CDKN1B, and MDM2) and 2 reference genes (SEM4F and CECR1). DNA copy number gains of MYC, CDK2, CDKN1B (p27kip1) and MDM2 are observed in an equal frequency (10%). Losses of DNA copies of RB1, CDNK2A, ATM, or TP53 are observed in 38, 31, 26, and 10 % of cases respectively. Some genes are almost exclusively gained (MYC,CDK2), deleted (RB1, ATM, TP53, CDNK2A) or both (CDK2, CDKN1B). Deletions of ATM and RB1 appear strongly associated (21% of cases, p=.001). CDKN2A (p14arf and p16ink4a) homozygous deletions and CDKN1B gains are more frequently observed in blastoid variants (p=.04 and .005 respectively). According to the MIPI score, the number of gene copy abnormalities tends to increase in the high/intermediate risk group (median = 1, range 0–6), as compared to the low risk group (median=0, range 0–3, p=.07). More specifically, MYC gain is exclusively observed in the high risk group (p=.04) and CDKN2A deletions are observed in patients with the highest MIPI. The prognostic relevance of the assay was tested in 42 patients. With a median follow-up of 22 months, CDK2 (3y OS=0%) or MDM2 (3y OS=0%) gains and CDKN2A (3y OS=20%) or TP53 (3y OS=25%) losses correlate to a shorter OS (p <.0001, p=.0007, p=.003 and p=.03 respectively). CDKN2A deletions remain predictive of the outcome in patient with a high MIPI (p =.0005). Furthermore, PCR performed in 5 cases at the time of relapse showed an increase of gene copy number abnormalities compared with initial diagnosis (median = 4 vs.1; p =.02), suggesting that gene losses/gains are involved in a dynamic and selected process. To conclude, we developed a reliable and routinely applicable PCR assay which delineates distinct MCL oncogenic pathways with strong prognostic impact that could be used in combination with the recently defined MIPI.

Development of a Multiplex PCR Assay for the Detection of Genomic Copy Number Changes in Myelodysplastic Syndromes

Background: Myelodysplastic syndrome (MDS) is a heterogeneous group of disorders characterized by ineffective hematopoiesis. Clonal cytogenetic aberrations are found in about 50% of primary MDS and 80% of secondary MDS. The International Prognostic Scoring System (IPSS) introduces cytogenetic abnormalities as an independent prognostic factor for both survival and progression to AML. However, conventional cytogenetics or FISH substitutes are not available for all myelodysplastic patients. In order to overcome this problem, we developed a multiplex PCR assay (quantitative multiplex PCR of short fluorescent fragments or QMPSF) measuring the copy number of genes located in regions involved in myelodysplastic syndromes on chromosome 7 and 8 and on the 5q, 12p, 17p and 20q regions.Material and method: In order to select target region, high resolution CGH (Agilent, 44K) was performed in 12 patients (5 complex karyotypes, 2 isolated monosomy 7, 2 isolated trisomy 8, 1 isolated 17p deletion, 1 isolated 20q deletion and 1 normal karyotype) for which DNA extracted from CD34+ sorted cells was available. Twenty three primer pairs were selected on 6 target chromosomes (5, 7, 8, 12, 17 and 20) in regions either commonly deleted or involved in biallelic deletions. A QMPSF assay was developed and applied on the first 12 patients. This assay was then applied on a series of 60 patients for which DNA extracted from either CD34 + sorted cells or total bone marrow (BM) cells or peripheral mononuclear cells (PB) was available.Results: As previously reported by several groups, the correlation between cytogenetics and CGH was very good although high resolution CGH was able to detect small cytogenetically not detected defects in most patients. For the 23 QMPSF targeted genes, the correlation between CGH log ratio and QMPSF ratio was excellent. Using QMPSF, genomic copy number changes were detected in 21/27 CD34+ samples, 16/20 BM samples and 15/20 PB samples. However, when different samples were available for the same patient (CD34, BM and/or PB) the correlation between samples was not perfect and mainly depends on the MDS subtype, the % of blasts and the presence of cytogenetics abnormalities.Conclusion: These results demonstrate that a single multiplex PCR assay targeting 23 genomic regions located on the 6 chromosomes most frequently involved in MDS can be helpful for the prognostic evaluation of MDS patients for whom cytogenetic data are not available, and that DNA extracted from PB or total BM cells can be informative in a substantial number of cases.

Detection of APC Gene Deletions Using Quantitative Multiplex PCR of Short Fluorescent Fragments

approximately 20% of classic familial adenomatous polyposis (FAP) cases and 70% to 80% of attenuated FAP (AFAP) cases are negative for the APC/MUTYH point mutation. Quantitative multiplex PCR of short fluorescent fragments (QMPSF), a technique for detecting copy number alterations, has been successfully applied to several cancer syndrome genes. We used QMPSF for the APC gene to screen FAP APC/MUTYH mutation-negative families to improve their diagnostic surveillance. we set up and validated APC-gene QMPSF using 23 negative and 1 positive control and examined 45 (13 FAP and 32 AFAP) unrelated members of APC/MUTYH mutation-negative families for copy number alterations. We confirmed the results using multiplex ligation-dependent probe amplification (MLPA). We used different approaches such as sequencing, quantitative real time-PCR (QRT-PCR), and fluorescence in situ hybridization (FISH) to further characterize the identified deletions. APC QMPSF was capable of detecting deletions with an acceptable variability, as shown by mean values (SD) of allele dosage for the deleted control obtained from intra- and interexperimental replicates [0.52 (0.05) and 0.45 (0.10)]. We detected 3 gross deletions in 13 (23%) of the classic FAP cases analyzed (1 complete gene deletion and 2 partial deletions encompassing exons 9 and 10 and exons 11-15, respectively). No rearrangements were detected in the 32 AFAP cases. QMPSF is able to detect rearrangements of the APC gene. Our findings highlight the importance of using a copy number alteration methodology as a first step in the routine genetic testing of FAP families in the clinical setting.

Deletion of the progranulin gene in patients with frontotemporal lobar degeneration or Parkinson disease

Progranulin gene ( PGRN) mutations cause ubiquitin-positive frontotemporal lobar degeneration linked to chromosome 17 (FTLDU-17). The spectrum of known mutations strongly suggests that neurodegeneration results from a partial loss of PGRN function and leads to the hypothesis that PGRN gene deletions could be present in a subset of patients. We analysed 63 unrelated French patients with frontotemporal lobar degeneration (FTLD) for PGRN gene dosage alteration by quantitative multiplex PCR of short fluorescent fragments (QMPSF). We identified in one patient with typical PGRN neuropathology a near complete deletion, removing exons 1–11, of the PGRN gene. This deletion, which resulted from a nonhomologous recombination event, was equally present in one affected sister presenting with Parkinson disease (PD). This observation provides a final argument that PGRN mutations exert their pathogenic effect through haploinsufficiency and underlines the diversity of clinical presentations associated with these PGRN alterations.

Non‐Hodgkin lymphoma related to hereditary nonpolyposis colorectal cancer in a patient with a novel heterozygous complex deletion in the MSH2 gene

Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal disorder caused by mutations in DNA mismatch repair (MMR) genes. Tumors of the HNPCC-spectrum are associated with microsatellite instability (MSI) and loss of MMR protein expression. Lymphomas are not considered to be HNPCC-related tumors. We report and analyze a case of an HNPCC patient with three colorectal cancers and a B-cell non-Hodgkin lymphoma. Quantitative multiplex PCR of short fluorescent fragments detected a novel MSH2 rearrangement involving exons 9 and 10, which proved to be the pathogenic cause of the disease in the family. Tumor tissues including the lymphoma showed MSI and loss of MSH2 expression. Multiplex ligation-dependent probe amplification analysis revealed a somatic loss of the wild-type MSH2 allele in the lymphoma. These results support the fact that the total loss of a MMR gene can lead to lymphomagenesis, as seen in biallelic MMR-deficient families and knockout mice. Moreover, this is the first report of a B-cell non-Hodgkin lymphoma with a loss of the MSH2 protein expression, linked to a heterozygous germline MSH2 mutation in an HNPCC family.

Detection of large rearrangements in the pheochromocytomas genes using QMPSF (quantitative multiplex PCR of short fluorescent fragments): improvement of genetic testing

Burnichon, Na; Strompf, La; Venisse, Aa; Drouot, Nb; Frebourg, Tb; Plouin, PFa; Jeunemaitre, Xa; Gimenez-Roqueplo, APa Author Information

Heterogeneity ofNSD1alterations in 116 patients with Sotos syndrome

Sotos syndrome is an overgrowth syndrome characterized by distinctive facial features, learning difficulties, and macrocephaly with frequent pre- and postnatal overgrowth with advanced bone age. Here, we report on our experience in the molecular diagnostic of Sotos syndrome on 116 patients. Using direct sequencing and a quantitative multiplex PCR of short fluorescent fragments (QMPSF)-based assay allowing accurate detection of both total and partial NSD1 deletions, we identified NSD1 abnormalities in 104 patients corresponding to 102 Sotos families (90%). NSD1 point mutations were detected in 80% of the index cases, large deletions removing the NSD1 gene entirely in 14%, and intragenic NSD1 rearrangements in 6%. Among the 69 detected distinct point mutations, 48 were novel. The QMPSF assay detected an exonic duplication and a mosaic partial deletion. QMPSF mapping of the 15 large deletions revealed the heterogeneity of the deletions, which vary in size from 1 to 4.5 Mb. Clinical features of NSD1-positive Sotos patients revealed that the phenotype in patients with nontruncating mutations was less severe that in patients with truncating mutations. This study confirms the heterogeneity of NSD1 alterations in Sotos syndrome and therefore the need to complete sequencing analysis by screening for partial deletions and duplications to ensure an accurate molecular diagnosis of this syndrome.

Partial duplications of the MSH2 and MLH1 genes in hereditary nonpolyposis colorectal cancer

Numerous reports have highlighted the contribution of MSH2 and MLH1 genomic deletions to hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch's syndrome, but genomic duplications of these genes have been rarely reported. Using quantitative multiplex PCR of short fluorescent fragments (QMPSF), 962 and 611 index cases were, respectively, screened for MSH2 and MLH1 genomic rearrangements. This allowed us to detect, in 11 families, seven MSH2 duplications affecting exons 1-2-3, exons 4-5-6, exon 7, exons 7-8, exons 9-10, exon 11, and exon 15, and three MLH1 duplications affecting exons 2-3, exon 4 and exons 6-7-8. All duplications were confirmed by an independent method. The contribution of genomic duplications of MSH2 and MLH1 to HNPCC can therefore be estimated approximately to 1% of the HNPCC cases. Although this frequency is much lower than that of genomic deletions, the presence of MSH2 or MLH1 genomic duplications should be considered in HNPCC families without detectable point mutations.

Contribution ofABCC6 genomic rearrangements to the diagnosis of pseudoxanthoma elasticum in French patients

Pseudoxanthoma elasticum (PXE) is an autosomal recessive disorder of connective tissues, which manifests with cutaneous, ophthalmologic and cardiovascular findings. PXE is caused by mutations in ABCC6 encoding a multidrug resistance protein (ABCC6, also known as MRP6). ABCC6 mutation detection rate ranges from 55% to 97% and it has been suggested that some of the remaining unidentified mutant alleles could correspond to large genomic rearrangements. In our cohort of 65 French PXE patients analysed for ABCC6 mutations, we identified two novel homozygous ABCC6 exonic deletions (deletions of exons 9-10 and exons 24-27). In order to systematically search for heterozygous genomic rearrangements, we have developed a quantitative multiplex PCR of short fluorescent fragments (QMPSF) approach that screens the 31 exons of ABCC6. We used QMPSF to analyse 13 PXE carrying at least one unidentified mutant, corresponding to 18 unidentified mutated alleles. This led to the detection of three large ABCC6 deletions, and two deletions of a single exon (exon 1 and exon 21). Thus QMPSF identified the causative mutation in 28% (5/18) of the uncharacterized ABCC6 mutant alleles in this cohort.

Novel genomic rearrangements in the BRCA1 gene detected in greek breast/ovarian cancer patients

The identification of genomic rearrangements in breast/ovarian cancer families has widened the mutational spectrum of the BRCA1 gene, increasing the number of patients who can benefit from molecular screening. More than 60 different BRCA1 genomic rearrangements with mapped breakpoints have been reported up to date, in all exons of the gene. The proportion of BRCA1 mutations due to genomic rearrangements varies from 8 to 27% in different populations, probably due to both ethnic diversity and the technical approach employed. In order to estimate the contribution of BRCA1 genomic rearrangements to hereditary breast/ovarian cancer (HBOC) predisposition in Greek families, probands from 95 families with breast/ovarian history but negative for point mutations or small insertions/deletions in BRCA1 and BRCA2 genes, were screened using Quantitative Multiplex PCR of Short Fluorescent Fragments (QMPSF). Two large deletions of 4.2 and 4.4 kb were identified in exons 20 and 24 respectively. Additional screening, using diagnostic primers for the above deletions in exons 20 and 24, performed on another 86 probands from families with breast/ovarian cancer history and 210 cases of sporadic breast/ovarian cancer resulted in the identification of two more large genomic rearrangements. One, identified in a familial case, identical to the previous exon 24 deletion and a second, identified in a case reported as sporadic, 3.2 kb deletion involving exon 20 and reported elsewhere in another Greek patient. Three out of four genomic rearrangements described in this study were detected in patients who had developed both breast and ovarian cancer; thus suggesting a correlation between the specific phenotype and the high probability of detecting inherited rearrangements in BRCA1.

A Quantitative Multiplex PCR Assay, Validated by a High Resolution Array Comparative Genomic Hybridization Analysis, Provides Information Regarding Genomic Imbalances and Prognosis in Diffuse Large B-Cell Lymphomas.

Genomic gains and losses may play a crucial role in the development and progression of diffuse large B-cell lymphomas (DLBCL). Some gains or losses are associated with particular morphologic or clinical manifestations and correlate with the “germinal center B-cell like” (GCB)/ non-GCB phenotype, as defined by gene expression profiles. To date, chromosomal-comparative genomic hybridization (CGH) and higher resolution array-CGH provide the more comprehensive view of these genomic imbalances. However, a CGH approach is expensive and not routinely applicable. By contrast, quantitative Multiplex PCR of Short Fluorescent Fragments (QMPSF) is an inexpensive and sensitive method for the detection of genomic deletions or duplications based on the simultaneous amplification of short genomic fragments using dye-labelled primers under quantitative conditions. We designed and evaluated a QMPSF assay to determine simultaneously frequencies of gain/loss of several genes and their clinical relevance in DLBCL. A series of 68 newly diagnosed DLBCL with available conventional cytogenetics and treated with anthracycline-based frontline therapy was studied (median age = 59 years, IPI 0–1: 35%; 2–3: 41%; 4–5: 24%). 15 cases were selected for both CGH (using a high resolution, high performance 60-mer oligonucleotide-based microarray that contains ~ 43,000 probes, with an average spatial resolution of 35 kB) and QMPSF experiments. Considering CGH as the reference method, and using primers located on chromosome 3q27 (BCL6), 6q16 (SIM1), 6q22 (PTPRK), 8q24 (MYC), 9p24 (JAK2), 9p21 (CDNK2A), 12q13 (cdk2), 12q15 (mdm2), 12p13.1 (p27) and 17p13 (p53), the sensibility and specificity of our QMPSF assay to detect abnormal DNA copy numbers ranged between 80–100% and 90–100% respectively. A gain of DNA copy numbers of MYC, p27, and BCL6 was observed in 19, 30 and 19 % respectively. Losses of DNA copies of p53 or CDNK2A were observed in 20 and 34 % of cases. Some genes were almost exclusively amplified (MYC, p27, cdk2) or exclusively deleted (p53, CDNK2A, PTPRK), indicating genomic imbalances selection during oncogenesis. Interestingly, 6q16 (SIM1), 6q22 (PTPRK) and 9p21 (CDNK2A) deletions were predominantly observed in the non-GCB subtype, whereas MYC gains were mainly observed in the GCB subtype and especially in de novo t(14;18) positive DLBCL (p =.002). The prognostic value of a QMPSF assay including 5 genes (p53, MYC, CDNK2A, SIM1 and p27) was tested. With a median follow-up of 81 months, detection of more than 2 gene copy number abnormalities was related to a worse event-free and overall survival (OS = 10 months, n = 13) as compared to patients with 0–2 abnormalities (OS not reached, p = .003, n = 55). The prognosis value of this PCR remains regardless the GCB/non-GCB subtype or the IPI score. To conclude, we developed a reliable and routinely applicable PCR assay, which provided information regarding gain/loss of relevant genes, and prognosis in DLBCL.

Comparison of a Quantitative PCR Method with FISH for the Assessment of the Four Aneuploïdies Commonly Evaluated in CLL Patients.

Four chromosomal defects associated with prognosis have been identified in CLL patients, namely deletions of the 13q13-q14, 11q22 and 17p13 regions and trisomy 12. Due to the low proliferation index of these tumors and to the fact that some defects can be cryptic, the detection of these abnormalities by conventional cytogenetics is difficult. Therefore, the resulting aneuploidies are usually evaluated by fluorescent in situ hybridisation (FISH). As probes are expensive and FISH time consuming, we aimed to compare a quantitative PCR method - quantitative PCR of short fluorescent fragments (QMPSF) - with FISH for the detection of these acquired aneuploidies in a series of 110 patients with Binet stage A CLL. Genes located in the deleted or gained regions were selected as target genes - DLEU2 at 13q14, ATM at 11q22, p53 at 17p13, POU6F1 and MDM2 at 12q13 and 12q15 respectively - and amplified using a method based on the simultaneous amplification of short fluorescent genomic fragments under quantitative conditions. A chromosomal imbalance involving one or several of the four loci was detected in 76 patients (69%) either by FISH or QMPSF or both. A deletion of chromosome 13 was found in 61 patients (55%). A 11q22 deletion was present in 9 patients (8%), a trisomy 12 in 9 (8%) and a 17p deletion in one. The rather low frequency of the three latter defects reflects the fact that only patients with stage A CLL at diagnosis were studied, and neither stage B or C CLL. The 13q deletion was isolated in 53 patients and associated with a second defect in 8: these were six of the 11q22 deletions, one trisomy 12 and the 17p deletion. When the 13q deletion was associated with either a 11q deletion or a trisomy 12 both abnormalities were present in the same proportion of cells. This was not the case for the 17p deletion which appeared to be a secondary event, since, as evaluated by FISH, it was present in 24% of cells whereas the 13q deletion was present in 85% of interphase nuclei. FISH and QMPSF results were identical for 103 of 110 patients. The secondary 17p deletion was not detected whereas all other discrepancies could be explained. This study demonstrates that a single multiplex PCR can replace FISH in CLL patients. However, whereas QMPSF is perfectly adapted to the detection of primary defects, care should be taken when searching for minor clonal evolutions present in a small proportion of tumor cells.

Simple detection of genomic microdeletions and microduplications using QMPSF in patients with idiopathic mental retardation

In contrast to the numerous well-known microdeletion syndromes, only a few microduplications have been described, and this discrepancy may be due in part to methodological bias. In order to facilitate the detection of genomic microdeletions and microduplications, we developed a new assay based on QMPSF (Quantitative Multiplex PCR of Short fluorescent Fragments) able to explore simultaneously 12 candidate loci involved in mental retardation (MR) and known to be the target of genomic rearrangements. We first screened 153 patients with MR and facial dysmorphism associated with malformations, or growth anomalies, or familial history, with cytogenetically normal chromosomes, and the absence of FRAXA mutation and subtelomeric rearrangements. In this series, we found a 5q35 deletion removing the NSD1 gene in a patient with severe epilepsy, profound MR and, retrospectively, craniofacial features of Sotos syndrome. In a second series, we screened 140 patients with MR and behaviour disturbance who did not fulfil the de Vries criteria for subtelomeric rearrangements and who had a normal karyotype and no detectable FRAXA mutation. We detected a 22q11 deletion in a patient with moderate MR, obesity, and facial dysmorphism and a 4 Mb 17p11 duplication in a patient with moderate MR, behaviour disturbance, strabismus, and aspecific facial features. This new QMPSF assay can be gradually upgraded to include additional loci involved in newly recognised microduplication/microdeletion syndromes, and should facilitate wide screenings of patients with idiopathic MR and provide better estimates of the microduplication frequency in the MR population.

Contribution of theBOP1 gene, located on 8q24, to colorectal tumorigenesis

The most common form of genomic instability observed in colorectal cancer is chromosomal instability (CIN), whose molecular bases remain to be determined. We have previously demonstrated that inactivation in human cells of several components of the Pes1-Bop1 complex (BOP1, GRWD1, PES1, ORC6L, and RPL3), involved in ribosome biogenesis, altered chromosome segregation. To determine the contribution to colorectal tumorigenesis of somatic alterations of genes involved in ribosome biogenesis, we screened 56 primary colorectal cancers, using quantitative multiplex PCR of short fluorescent fragments, a sensitive method for the detection of gene dosage alterations. We found that dosage increase of the BOP1 gene was a frequent event, being detected in 39% of the tumors, and we show that it is associated with an increase of BOP1 mRNA. Scanning of 8q24, on which BOP1 is located, revealed that in colorectal cancers, gene dosage increase of BOP1 can be independent from that of MYC and was more frequent than that affecting MYC. Finally, transient overexpression of BOP1 in human cells increased the percentage of multipolar spindles. Together with our previous results, the present study strongly suggests that deregulation of the BOP1 pathway contributes to colorectal tumorigenesis.

Molecular evaluation of foetuses with holoprosencephaly shows high incidence of microdeletions in the HPE genes

Holoprosencephaly (HPE), the most common structural malformation of the forebrain in humans, can be detected early during pregnancy using prenatal ultrasonography . Among foetuses with a normal karyotype, 14% have mutations in the four main HPE genes (SHH, ZIC2, SIX3 and TGIF). Genomic rearrangements have now been implicated in many genetic diseases, so we hypothesized that microdeletions in the major HPE genes may also be common in HPE foetuses with severe phenotype or other associated malformations. We screened the DNA obtained from 94 HPE foetuses with a normal karyotype for the presence of microdeletions involving the four major HPE genes (SHH, ZIC2, SIX3 and TGIF). Thirteen of the foetuses had a point mutation in one of the 4 genes and 81 had no known mutations. Quantitative multiplex PCR of short fluorescent fragments (QMPSF) analysis was used for rapid determination of HPE genes copy numbers and the identified microdeletions were confirmed by real time quantitative PCR, or fluorescent in situ hybridization (FISH) (if a cell line was available). Microdeletions were detected in 8 of 94 foetuses (8.5%) (2 in SHH, 2 in SIX3, 3 in ZIC2 and 1 in TGIF genes), and only among the 81 foetuses with a normal karyotype and no point mutations. These data suggest that microdeletions in the four main HPE genes are a common cause of prenatal HPE, as well as point mutations, and increase the total diagnosis rate close to approximately 22.3% of foetuses with normal karyotype. Detection can be achieved by the QMPSF testing method that proved to be efficient for testing several genes in a single assay.

Golli‐MBP Copy Number Analysis by FISH, QMPSF and MAPH in 195 Patients with Hypomyelinating Leukodystrophies

The inherited disorders of CNS myelin formation represent a heterogeneous group of leukodystrophies. The proteolipoprotein (PLP1) gene has been implicated in two X-linked forms, Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia type 2, and the gap junction protein alpha12 (GJA12) gene in a recessive form of PMD. The myelin basic protein (MBP) gene, which encodes the second most abundant CNS myelin protein after PLP1, presents rearrangements in hypomyelinating murine mutants and is always included in the minimal region deleted in 18q- patients with an abnormal hypomyelination pattern on cerebral MRI. In this study, we looked at the genomic copy number at the Golli-MBP locus in 195 patients with cerebral MRI suggesting a myelin defect, who do not have PLP1 mutation. Although preliminary results obtained by FISH suggested the duplication of Golli-MBP in 3 out of 10 patients, no abnormal gene quantification was found using Quantitative Multiplex PCR of Short Fluorescent fragments (QMPSF), Multiplex Amplifiable Probe Hybridization (MAPH), or another FISH protocol using directly-labelled probes. Pitfalls and interest in these different techniques to detect duplication events are emphasised. Finally, the study of this large cohort of patients suggests that Golli-MBP deletion or duplication is rarely involved in inherited defects of myelin formation.