Predicting 1p/19q codeletion status using diffusion-, susceptibility-, perfusion-weighted, and conventional MRI in IDH-mutant lower-grade gliomas.

BACKGROUND: Isocitrate dehydrogenase (IDH)-mutant lower-grade gliomas (LGGs) are further classified into two classes: with and without 1p/19q codeletion. IDH-mutant and 1p/19q codeleted LGGs have better prognosis compared with IDH-mutant and 1p/19q non-codeleted LGGs. PURPOSE: To evaluate conventional magnetic resonance imaging (cMRI), diffusion-weighted imaging (DWI), susceptibility-weighted imaging (SWI), and dynamic susceptibility contrast perfusion-weighted imaging (DSC-PWI) for predicting 1p/19q codeletion status of IDH-mutant LGGs. MATERIAL AND METHODS: We retrospectively reviewed cMRI, DWI, SWI, and DSC-PWI in 142 cases of IDH mutant LGGs with known 1p/19q codeletion status. Features of cMRI, relative ADC (rADC), intratumoral susceptibility signals (ITSSs), and the value of relative cerebral blood volume (rCBV) were compared between IDH-mutant LGGs with and without 1p/19q codeletion. Receiver operating characteristic curve and logistic regression were used to determine diagnostic performances. RESULTS: IDH-mutant and 1p/19q non-codeleted LGGs tended to present with the T2/FLAIR mismatch sign and distinct borders (P < 0.001 and P = 0.038, respectively). Parameters of rADC, ITSSs, and rCBVmax were significantly different between the 1p/19q codeleted and 1p/19q non-codeleted groups (P < 0.001, P = 0.017, and P < 0.001, respectively). A combination of cMRI, SWI, DWI, and DSC-PWI for predicting 1p/19q codeletion status in IDH-mutant LGGs resulted in a sensitivity, specificity, positive predictive value, negative predictive value, and an AUC of 80.36%, 78.57%, 83.30%, 75.00%, and 0.88, respectively. CONCLUSION: 1p/19q codeletion status of IDH-mutant LGGs can be stratified using cMRI and advanced MRI techniques, including DWI, SWI, and DSC-PWI. A combination of cMRI, rADC, ITSSs, and rCBVmax may improve the diagnostic performance for predicting 1p/19q codeletion status.

PXK locus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility gene ABHD6.

OBJECTIVES: To perform fine mapping of the PXK locus associated with systemic lupus erythematosus (SLE) and study functional effects that lead to susceptibility to the disease. METHODS: Linkage disequilibrium (LD) mapping was conducted by using 1251 SNPs (single nucleotide polymorphism) covering a 862 kb genomic region on 3p14.3 comprising the PXK locus in 1467 SLE patients and 2377 controls of European origin. Tag SNPs and genotypes imputed with IMPUTE2 were tested for association by using SNPTEST and PLINK. The expression QTLs data included three independent datasets for lymphoblastoid cells of European donors: HapMap3, MuTHER and the cross-platform eQTL catalogue. Correlation analysis of eQTLs was performed using Vassarstats. Alternative splicing for the PXK gene was analysed on mRNA from PBMCs. RESULTS: Fine mapping revealed long-range LD (>200 kb) extended over the ABHD6, RPP14, PXK, and PDHB genes on 3p14.3. The highly correlated variants tagged an SLE-associated haplotype that was less frequent in the patients compared with the controls (OR=0.89, p=0.00684). A robust correlation between the association with SLE and enhanced expression of ABHD6 gene was revealed, while neither expression, nor splicing alterations associated with SLE susceptibility were detected for PXK. The SNP allele frequencies as well as eQTL pattern analysed in the CEU and CHB HapMap3 populations indicate that the SLE association and the effect on ABHD6 expression are specific to Europeans. CONCLUSIONS: These results confirm the genetic association of the locus 3p14.3 with SLE in Europeans and point to the ABHD6 and not PXK, as the major susceptibility gene in the region. We suggest a pathogenic mechanism mediated by the upregulation of ABHD6 in individuals carrying the SLE-risk variants.

Triorchidism: genetic and imaging evaluation in an adult male.

We report the results of imaging and cytogenetic studies in a case of triorchidism in a 54 years old male without any associated anomaly. A scrotal ultrasonography revealed the presence of two testes within the left hemiscrotum with complete septation and echotexture and vascular flow pattern similar to the vascular flow of the normal right testis. There was no focal abnormal echogenicity suggesting malignancy. Scrotal MRI confirmed two soft-tissue structures in the left hemiscrotum with normal signal intensity at T1w and T2w images. Both testes had a tunica albuginea with low-signal intensity. Cytogenetic analysis resulted in normal male karyotype 46XY. Array-CGH analysis detected the presence of two interstitial rearrangements: a ~120 Kb deletion of chromosome 1 and a ~140 Kb deletion of chromosome 16. Currently there are little details on the functions of both genes.

HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia.

BACKGROUND: The development of cervical cancer and its high-grade precursor lesions (Cervical Intraepithelial Neoplasia grade 2/3 [CIN2/3]) result from a persistent infection with high-risk human papillomavirus (hrHPV) types and the accumulation of (epi)genetic host cell aberrations. Epidemiological studies have demonstrated variable CIN2/3 and cancer risks between different hrHPV types. Recent genomic profiling studies revealed substantial heterogeneity in the chromosomal aberrations detected in morphologically indistinguishable CIN2/3 suggestive of varying cancer risk. The current study aimed to investigate whether CIN2/3 with different hrHPV types vary with respect to their chromosomal profiles, both in terms of the number of aberrations and chromosomal loci affected. METHODS: Chromosomal profiles were determined of 43 p16INK4a-immunopositive CIN2/3 of women with long-term hrHPV infection (≥ 5 years). Sixteen lesions harboured HPV16, 3 HPV18, 14 HPV31, 1 HPV33, 4 HPV45, 1 HPV51, 2 HPV52 and 2 HPV58. RESULTS: Unsupervised hierarchical clustering analysis of the chromosomal profiles revealed two major clusters, characterised by either few or multiple chromosomal aberrations, respectively. A majority of 87.5% of lesions with HPV16 were in the cluster with relatively few aberrations, whereas no such unbalanced distribution was seen for lesions harbouring other hrHPV types. Analysis of the two most prevalent types (HPV16 and HPV31) in this data set revealed a three-fold increase in the number of losses in lesions with HPV31 compared to HPV16-positive lesions. In particular, losses at chromosomes 2q, 4p, 4q, 6p, 6q, 8q & 17p and gain at 1p & 1q were significantly more frequent in HPV31-positive lesions (FDR < 0.2). CONCLUSIONS: Chromosomal aberrations in CIN2/3 are at least in part related to the hrHPV type present. The relatively low number of chromosomal aberrations observed in HPV16-positive CIN2/3 suggests that the development of these lesions is less dependent on genetic insult than those caused by other types like HPV31.

Refractory neonatal epilepsy with a de novo duplication of chromosome 2q24.2q24.3.

There are only two reports on epileptic patients associated with microduplication of 2q. We found a de novo duplication of chromosome 2q24.2q24.3 in another infant with neonatal epilepsy. The patient had refractory focal seizures since the third day of life. Her seizures were refractory against phenobarbital and levetiracetam, but were controlled by valproate. Array comparative genomic hybridization revealed a 5.3-Mb duplication of 2q24.2q24.3, where at least 22 genes including a cluster of voltage-gated sodium channel genes (SCN1A, SCN2A, SCN3A, SCN7A, and SCN9A) and one noncoding RNA are located.

Natural history and long-term evolution in families with autosomal dominant cortical tremor, myoclonus, and epilepsy.

PURPOSE: To investigate for the first time the natural history and long-term evolution of "familial cortical tremor, myoclonus, and epilepsy." METHODS: We evaluated the clinical, electrophysiologic, and treatment data of 14 patients from three families linked to 2p11.1-q12.2. A simplified scale was used to score myoclonus severity. Electroencephalography (EEG) studies were reviewed for the evaluation of background activity, paroxysmal abnormalities, and photoparoxysmal response. Data were organized for age groups. Correlation and logistic regression analysis were performed. KEY FINDINGS: Patients' mean age was 47.8 ± 22.0 years (range 20-86 years). Mean age at disease onset was 20.2 ± 7.8 years (range 11-40 years); mean follow-up duration was 14.0 ± 5.8 years (range 7-28 years). Evaluation at different age groups revealed a gradual, progressive worsening of the myoclonus in 10 patients (71.4%). Two subjects aged >80 years showed myoclonus interfering with autonomous walking. Myoclonus severity was correlated with disease duration (p<0.001) and patients' age (p=0.001). Six patients (42.8%) experienced seizures, usually between the second and sixth decades of life. Evaluation of EEG long-term evolution revealed progressive slowing of background activity in parallel with the gradual worsening of myoclonus. In contrast, paroxysmal activity and photosensitivity were particularly evident during the intermediate phases of the disease. In addition, psychiatric and neuropsychological dysfunction occurred in more than one third of the patients. SIGNIFICANCE: We provide data for a slight age-dependent progression and the presence of neuropsychiatric and neuropsychological dysfunction in this unique syndrome, for which the definition of familial or autosomal dominant cortical tremor, myoclonus, and epilepsy (FCTME/ADCME) seems to be, therefore, more appropriate.

[Chromosomal location of nonsyndromic cleft lip with or without palates for two multiplex families].

OBJECTIVE: To find chromosome region closely linked to nonsyndromic cleft lip with or without palates (NSCL±P) by genome-wide scan and linkage analysis for two multiplex families. METHODS: Whole-genome scan and fine genome scan were used to analyse multiplex families members, and parametric, nonparametric and interaction statistical analysis software to determine which chromosomal section was linked to the genetic disease. RESULTS: Both parametric and nonparametric linkage scores increased by a big margin over the initial linkage scores on 1q32.2-41. Although parametric results were not significant, nonparametric linkage gave a strong evidence for a candidate region on chromosome 2p25.1-24.2. The multiplicative model gave the strongest evidence for interaction in 1q32.2-41 and 2p25.1-24.2. CONCLUSION: Parametric and nonparametric linkage analyses for 2 NSCL±P multiplex families show that there may be candidate regions on chromosome 1q32.2-41 and 2p25.1-24.2.The two regions of 1q32.2-41 and 2p25.1-24.2 may contribute to NSCL±P risks with interaction.

Multiple human beta interferon genes.

Analysis of human beta interferon (IFN) mRNA preparations obtained from poly(I) . poly (C)-induced human diploid fibroblasts (FS-4) and from several similarly induced human-mouse somatic cell hybrids by electrophoresis through agarose-CH3HgOH tube gels led to the detection of at least five translationally active human IFN-beta mRNA species. The results obtained are consistent with the existence of IFN-beta genes on different human chromosomes. Marked cell-dependent variability in the expression of these IFN mRNA species was observed.

Chromosomal location of human kappa and lambda immunoglobulin light chain constant region genes.

The chromosomal location of human constant region light chain immunoglobulin (Ig) genes has been determined by analyzing a group of human fibroblast/rodent somatic cell hybrids with nucleic acid probes prepared from cloned human kappa and lambda constant region genes. Human chromosomes in each cell line were identified by isoenzyme analysis. The DNA from hybrid cells was digested with restriction endonucleases, size fractionated by gel electrophoresis, transferred to nitrocellulose or DBM paper, and hybridized with (32)P-labeled nucleic acid probes. The C(kappa) gene was assigned to human chromosome 2 and the C(lambda) genes to chromosome 22, based upon analysis of these hybrid cell lines, and these assignments were confirmed by analysis of subclones. A group of previously unassigned loci can be mapped to chromosome 2 by virtue of their close linkage to C(kappa). The lambda and kappa light chain and heavy chain Ig genes have now been assigned to all three human chromosomes that are involved in translocations with chromosome 8 in human B cell neoplasms. These techniques and probes provide a means to study the detailed arrangement of human Ig genes and their pseudogenes.

Gene for the human T cell differentiation antigen Leu-2/T8 is closely linked to the kappa light chain locus on chromosome 2.

We have mapped the gene encoding the T cell differentiation antigen Leu-2/T8 to human chromosome 2 by hybridization of a Leu-2/T8 complementary DNA clone to DNA from a panel of mouse-human cell hybrids. In situ hybridization further localizes the gene to the 2p1 region in close proximity to the Ig kappa light chain gene. The Leu-2/T8 gene translocates with C kappa to chromosome 8 in a Burkitt lymphoma line carrying a t(2;8) translocation. These data support the hypothesis that Leu-2/T8 is the human homologue of the mouse Lyt-2,3 antigen.

Development and successful clinical application of preimplantation genetic haplotyping for Herlitz junctional epidermolysis bullosa.

BACKGROUND: Herlitz junctional epidermolysis bullosa (HJEB) is a severe, life-threatening, autosomal recessive blistering skin disease for which no cure is currently available. Prenatal diagnosis for couples at risk is feasible through fetal skin biopsy or analysis of DNA extracted from chorionic villi, but these methods can be applied only after pregnancy has been established. An alternative approach, which involves the analysis of single cells from embryos prior to establishment of pregnancy, is preimplantation genetic diagnosis (PGD). Until now, its clinical uptake has been hindered by lengthy delays in establishing mutation-specific protocols, and by the small amount of template DNA that can be obtained from a single cell. A new method that addresses these problems, preimplantation genetic haplotyping (PGH), relies on whole genome amplification followed by haplotyping of multiple polymorphic markers using standard DNA-based polymerase chain reaction (PCR) assays. OBJECTIVES: To design and validate a generic PGH assay for HJEB and to transfer this into clinical practice. MATERIALS AND METHODS: We established a multiplex PCR-based PGH assay involving 16 markers within and flanking the LAMB3 gene (the most frequently mutated gene in HJEB). The assay was then validated in 10 families with at least one previously affected offspring. After licensing by the Human Fertilisation and Embryology Authority (HFEA), the new test was used for PGD in a couple at risk of HJEB. RESULTS: The chromosome 1 LAMB3 markers within the assay were shown to be of sufficient heterogeneity to have widespread application for preimplantation testing of HJEB. In one couple that were heterozygous carriers of nonsense mutations in LAMB3, we used the new assay to identify unaffected embryos in a series of PGD cycles. Pregnancy was established in the third PGD cycle and a healthy, unaffected child was born. DNA analysis of cord blood confirmed the predicted single-cell mutation status of wild-type LAMB3 alleles. CONCLUSIONS: PGH represents a major step forward in widening the scope and availability of preimplantation testing for serious mapped single-gene disorders. We have established a generic test that is suitable for the majority of couples at risk of HJEB.

[Successful rituximab monotherapy in a patient with mucosa-associated lymphoid tissue lymphoma of the rectum with trisomy 3, 18].

A 62-year-old man was referred to our hospital with enlargement of mucosa-associated lymphoid tissue (MALT) lymphoma of the rectum after the eradication of Helicobacter pylori. The patient was given a diagnosis of stage I MALT. Endoscopic observation revealed an enlarged rectal tumor with 3, 18 double trisomy. Rituximab monotherapy was given and complete remission was achieved. Rituximab monotherapy can be useful for MALT lymphoma of the rectum.

Mapping human autosomes: assignment of the MN locus to a specific segment in the long arm of chromosome no. 2.

The locus for MN blood groups, MN, is tentatively assigned to a specific region near the centromere of the long arm of chromosome No. 2 on the basis of a demonstrable deletion of band 2q14 from a No. 2 chromosome in a boy previously reported to be hemizygous (M/-) at that locus.

Specific chromosome defect associated with human small-cell lung cancer; deletion 3p(14-23).

A specific, acquired chromosomal abnormality (deletion 3p) has been found in at least one chromosome 3 in 100 percent of the metaphases in 12 of 12 cell lines cultured from human small-cell lung cancer tissue and in 2-day tumor culture specimens from three patients. Analysis of the shortest region of overlap shows the deletion to be 3p(14-23). This specific change was not seen in five of five lung cancer cell lines other than small-cell lung cancer or in two lymphoblastoid lines cultured from cells of small-cell lung cancer patients whose tumors had the 3p deletion.

Giemsa-11 staining of chromosome 1: a newly described heteromorphism.

Sequential Giemsa-11 and C-band staining of the heterochromatic region of chromosome 1 from 30 unrelated individuals revealed a high degree of variability within this region, more than was identifiable with either stain alone. The Giemsa-11 stained material usually appeared as a single band of only slightly varying size within the heterochromatic region. The position of this band ranged from a location immediately adjacent to the centromere, to one farther along the long arm or at the junction of the C-band heterochromatin and euchromatin. Two individuals had a chromosome 1 with no detectable Giemsa-11 band but an average-size C-band. Two others with a large heterochromatic segment by C-banding had two Giemsa-11 positive bands. Additional studies of five members of one family were consistent with transmission of these hetermorphisms in codominant Mendelian fashion.

Tissue factor gene localized to human chromosome 1 (1pter----1p21).

Tissue factor (tissue thromboplastin, coagulation factor III), a protein component of cell membranes, is an essential cofactor for factor VII-dependent initiation of blood coagulation. Since no tissue factor-deficient condition has been described, it is one of only a few proteins of the coagulation system for which the pattern of inheritance has not been ascertained. Because of the species-specificity of tissue factor activity and the availability of a very sensitive chromogenic assay, it was possible in the present study to use somatic cell hybrids to assign the chromosomal location of the tissue factor structural gene (F3) to human chromosome 1 (1pter----1p21).

Molecular analysis of the t(2;14) translocation of childhood chronic lymphocytic leukemia.

Two rare cases of chronic lymphocytic leukemia (CLL) in children have been studied; both are associated with a previously undescribed chromosomal translocation [t(2;14) (p13;q32)]. In one patient the translocation was reciprocal and the breakpoint on chromosome 14 occurred just 5' of the C gamma 2 region on the productive immunoglobulin heavy-chain allele. The breakpoint on chromosome 2 does not involve the K locus but lies within an uncharacterized region that coincides with the position of a constitutive fragile site that occurs within normal lymphocytes. Data on the second patient are consistent with these findings and suggest that these cases represent a rare but distinct subgroup of CLL's with a specific cytogenetic change.

The human gene for the beta subunit of nerve growth factor is located on the proximal short arm of chromosome 1.

Fragments of the recently cloned human gene for the beta subunit of nerve growth factor (beta-NGF) were used as hybridization probes in analyzing two sets of rodent-human somatic cell hybrids for the presence of human beta-NGF sequences. Results from the first set of hybrids assigned the human beta-NGF gene to chromosome 1 and ruled out the presence of sequences of comparable homology on any other chromosome. With the second set of hybrids, which contained seven different, but overlapping, regions of chromosome 1, the NGF locus was mapped to band 1p22.

Polymorphism of human constitutive heterochromatin.

Genetic polymorphism has been demonstrated in man for many characteristics including blood groups, serum proteins, tissue enzymes, and hemoglobins. A class of chromosomal polymorphism involving constitutive heterochromatin has now been found. Through the use of a special technique that permits visualization of heterochromatin, seven heterochromatin variants have been found among four individuals. These results suggest a very high frequency of variability of heterochromatin in the population.

Mapping of the human Blym-1 transforming gene activated in Burkitt lymphomas to chromosome 1.

Blym-1, a transforming gene detected by transfection of NIH 3T3 cells with DNA from Burkitt lymphomas, was mapped to the short arm of chromosome 1 (1p32) by chromosomal in situ hybridization. The Blym-1 gene was not physically linked to the cellular myc oncogene or to any of the immunoglobulin gene loci implicated in the characteristic chromosomal translocations in Burkitt lymphoma.