[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.

Proficiency testing of human leukocyte antigen-DR and human leukocyte antigen-DQ genetic risk assessment for type 1 diabetes using dried blood spots

BACKGROUND

The plurality of genetic risk for developing type 1 diabetes mellitus (T1DM) lies within the genes that code for the human leukocyte antigens (HLAs). Many T1DM studies use HLA genetic risk assessment to identify higher risk individuals, and they often conduct these tests on dried blood spots (DBSs) like those used for newborn bloodspot screening. One such study is The Environmental Determinants of Diabetes in the Young (TEDDY), a long-term prospective study of environmental risk factors. To provide quality assurance for T1DM studies that employ HLA genetic risk assessment, the Centers for Disease Control and Prevention (CDC) conducts both a voluntary quarterly proficiency testing (VQPT) program available to any laboratory and a mandatory annual proficiency testing (PT) challenge for TEDDY laboratories.

METHODS

Whole blood and DBS samples with a wide range of validated HLA-DR and HLA-DQ genotypes were sent to the participating laboratories. Results were evaluated on the basis of both the reported haplotypes and the HLA genetic risk assessment.

RESULTS

Of the reported results from 24 panels sent out over six years in the VQPT, 94.7% (857/905) were correctly identified with respect to the relevant HLA-DR or HLA-DQ alleles, and 96.4% (241/250) were correctly categorized for risk assessment. Significant improvement was seen over the duration of this program, usually reaching 100% correct categorization during the last three years. Of 1154 reported results in four TEDDY PT challenges, 1153 (99.9%) were correctly identified for TEDDY eligibility.

CONCLUSIONS

The different analytical methods used by T1DM research centers all provided accurate (>99%) results for genetic risk assessment. The two CDC PT programs documented the validity of the various approaches to screening and contributed to overall quality assurance.

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.

Irinotecan Toxicity to Human Blood Cells in vitro: Relationship between Various Biomarkers

Toxic effects of the antineoplastic drug irinotecan on human blood cells at concentrations of 9.0 microg/ml and 4.6 microg/ml were evaluated in vitro. Using the alkaline and neutral comet assay significantly increased levels of primary DNA damage in lymphocytes were detected. The induction of apoptosis/necrosis, as determined by a fluorescent assay, was also notably increased. Cytogenetic outcomes of the treatment were assessed by the analysis of structural chromosome aberrations and fluorescence in situ hybridization. A significantly higher incidence of chromatid breaks and complex quadriradials was observed. Painted chromosomes 1, 2 and 4 were equally involved in translocations, but only the chromosome 1 was involved in the formation of quadriradials. Sister chromatid exchange analysis was performed in parallel with the analysis of lymphocyte proliferation kinetics. The higher concentration of irinotecan caused almost seven-time increase, while the lower one caused a five-time increase of the basal sister chromatid exchange frequency, accompanied with significant lowering of the lymphocyte proliferation index. Using the cytokinesis-block micronucleus assay, a dose-dependent increase in micronucleus frequency along with the formation of nuclear buds and nucleoplasmic bridges was noticed. Inhibitory effects of irinotecan on enzyme acetylcholinesterase (AChE) were studied in erythrocytes. An IC(50) value of 5.0 x 10(-7) was established. Irinotecan was found to be strong inhibitor of the acetylcholine hydrolysis and to cause a continuous decrease of catalytic activity of AChE. The results obtained on a single donor may contribute to the understanding of irinotecan toxicity, but further in vitro and in vivo studies are essential in order to clarify remaining issues, especially on possible inter-individual variability in genotoxic responses to the drug.

Primary ovarian failure in a mentally retarded woman with a de novo unbalanced X;autosome translocation

OBJECTIVE

To describe the clinical findings of a patient with a de novo unbalanced X;autosome translocation.

DESIGN

Descriptive case study.

SETTING

Mackay Memorial Hospital, National Yang-Ming University, China Medical University, China Medical University Hospital, and Chung Shan Medical University.

PATIENT(S)

A 33-year-old woman with primary ovarian failure, moderate mental retardation, and mild phenotype of facial dysmorphism.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Ultrasound, cytogenetic analysis, and laboratory studies of hormones.

RESULT(S)

Laboratory studies revealed the following values: FSH level 72.48 mIU/mL (normal women: <40 mIU/mL), LH level 32.87 mIU/mL (normal women: <21 mIU/mL), and E(2) level <20 pg/mL (normal women up to 375 pg/mL), confirming primary ovarian failure. The PRL level was normal. Spectral karyotyping and G-banding cytogenetic analysis revealed a derivative X chromosome containing additional chromosomal material derived from the distal long arm of chromosome 5. The derived chromosome X had break points at Xq27.3 and 5q32, resulting in monosomy Xq (Xq27.3-->qter) and partial trisomy 5q (5q32-->qter). The patient's karyotype was 46,X,der(X)t(X;5)(q27.3;q32). The parental karyotypes were normal.

CONCLUSION(S)

This is the first report of partial monosomy Xq (Xq27.3-->qter) and partial trisomy 5q (5q32-->qter). The present case provides evidence for the occurrence of primary ovarian failure and mental retardation in females with unbalanced X;autosome translocations.

TBLR1 regulates the expression of nuclear hormone receptor co-repressors

Background

Transcription is regulated by a complex interaction of activators and repressors. The effectors of repression are large multimeric complexes which contain both the repressor proteins that bind to transcription factors and a number of co-repressors that actually mediate transcriptional silencing either by inhibiting the basal transcription machinery or by recruiting chromatin-modifying enzymes.

Results

TBLR1 [GenBank: NM024665] is a co-repressor of nuclear hormone transcription factors. A single highly conserved gene encodes a small family of protein molecules. Different isoforms are produced by differential exon utilization. Although the ORF of the predominant form contains only 1545 bp, the human gene occupies ~200 kb of genomic DNA on chromosome 3q and contains 16 exons. The genomic sequence overlaps with the putative DC42 [GenBank: NM030921] locus. The murine homologue is structurally similar and is also located on Chromosome 3. TBLR1 is closely related (79% homology at the mRNA level) to TBL1X and TBL1Y, which are located on Chromosomes X and Y. The expression of TBLR1 overlaps but is distinct from that of TBL1. An alternatively spliced form of TBLR1 has been demonstrated in human material and it too has an unique pattern of expression. TBLR1 and the homologous genes interact with proteins that regulate the nuclear hormone receptor family of transcription factors. In resting cells TBLR1 is primarily cytoplasmic but after perturbation the protein translocates to the nucleus. TBLR1 co-precipitates with SMRT, a co-repressor of nuclear hormone receptors, and co-precipitates in complexes immunoprecipitated by antiserum to HDAC3. Cells engineered to over express either TBLR1 or N- and C-terminal deletion variants, have elevated levels of endogenous N-CoR. Co-transfection of TBLR1 and SMRT results in increased expression of SMRT. This co-repressor undergoes ubiquitin-mediated degradation and we suggest that the stabilization of the co-repressors by TBLR1 occurs because of a novel mechanism that protects them from degradation. Transient over expression of TBLR1 produces growth arrest.

Conclusion

TBLR1 is a multifunctional co-repressor of transcription. The structure of this family of molecules is highly conserved and closely related co-repressors have been found in all eukaryotic organisms. Regulation of co-repressor expression and the consequent alterations in transcriptional silencing play an important role in the regulation of differentiation.

Translocation (3;12) (p21-pter; q24.1-qter) and phenylketonuria

Cytogenetic karyotyping in mental retardation associated with physical dysmorphism has been regarded as the primary key for the classification of syndromes and other genetic disorders for the predisposition of neoplasia and other fatal diseases. Giemsa-banding of metaphase chromosomes in lymphocytes is a traditional and routine process for the identification of the chromosomal counterpart which can provide a clue for molecular investigation in the subject. An 8-year-old girl showed a diploid karyotype 46, XX, t(3;12) (p21-pter, q24.1-qter) in peripheral blood lymphocyte culture. Biochemical examination of urine labelled her as a case of phenylketonuria. The maternal karyotyping was similar and confirmed the maternal transmission of the translocation.

Cytogenetic characterization of Ewing tumors using fine needle aspiration samples. a 10-year experience and review of the literature

Chromosomal analysis was performed in fine needle aspiration samples of 98 primary Ewing tumors (ETs) prior to treatment. Among the 58 (59.18%) successful cultures, t(11;22)(q24;q12) was observed in 87.9% and 6.8% had abnormalities other than t(11;22), viz., del(22)(q12), der(16)t(1;16)(q12;q11), and variant t(8;22)(q24;q12). Involvement of breakpoints 1q21, 1q22, 3p14, 16q22, and 17p13 was also observed. Numerical abnormalities such as trisomies 8 and 12 were found in 29.3% and 20.6% and trisomy 18 in 17.2%. An attempt was made to evaluate the role of these additional changes in the process of tumor development, metastasis, and progression of the disease. This is the largest cytogenetic study on ET from a single center using a simple and reliable technique of fine-needle aspiration culture. The literature on cytogenetics of ET is reviewed.

Assessment of genomic imbalances in malignant fibrous histiocytomas by comparative genomic hybridization

In order to investigate genomic imbalances, comparative genomic hybridization was applied to 20 malignant fibrous histiocytomas. Deletions were rare and found mainly in chromosomes 2q33-35, 4q32-qter, 8p, 9p21-pter, 12p and 19p, whereas, over-representations frequently affected chromosomes 3, 4q31, 5p, 6, 7, 14q22-ter, 18p, as well as, five distinct amplifications within the regions 12q12-15 and 15q24-qter. The total number of genetic imbalances per tumor was slightly increased in primary tumors when compared to relapses. No relationship was found between the patterns of gain and loss when compared to the histological subtype, tumor grading, the clinical outcome and the p53 mutation status.

Systematic search for uniparental disomy in early fetal losses: the results and a review of the literature

About 20% of all human conceptuses are estimated to be trisomic and trisomy of all chromosomes remains a common cause of early fetal loss. Uniparental disomy (UPD) has been reported for most human chromosomes and may be an underrecognized contributor to embryonic lethality. To investigate the contribution of UPD to spontaneous abortions, we devised a genome-based screening strategy to identify holochromosomic UPD in 18 fetal losses. No cases of UPD were identified using this approach. Based on our data, UPD does not appear to be a significant contributor to early embryonic lethality. The results of the study are presented along with a review of the cases of UPD reported in the literature by chromosome, parental origin, mode of ascertainment, and phenotypic consequences due to imprinting.

Allelotyping demonstrates common and distinct patterns of chromosomal loss in human lung cancer types

Allelic loss is a hallmark of tumor suppressor gene (TSG) inactivation. We have allelotyped 29 paired lymphoblastoid and lung cancer cell lines derived from 11 patients with small cell (SCLC) and 18 patients with non-small cell lung carcinomas (NSCLC). Statistical analysis indicated that a threshold of 30% separated non-random allelic loss from the random genetic deletions of malignancy. We have identified non-random allelic loss at 42 of 54 (78%) specific chromosomal regions examined, with 22 regions (52%) common between the two major lung cancer histologic types. There were 3 regions (7%) with allelic loss specific for SCLC and 17 regions (41%) specific for NSCLC. Furthermore, there were significant differences in loss of heterozygosity (LOH) frequencies between NSCLC and SCLC at 13 regions on eight chromosome arms (3p, 5q, 6q, 9p, 10q, 11p, 13q, and 19p). Eight homozygous deletions were present in seven cell lines at four regions, 3p12, 3p14.2, 9p21, and 10q23-25. We have also identified novel sites of chromosomal deletions. In particular, there was frequent loss at 11p13 in SCLC and loss at 6p21.3 and 13q12.3 in NSCLC. In this study, we demonstrate that a) non-random allelic losses in lung cancer involve multiple regions; b) some losses are common to both NSCLC and SCLC subtypes, whereas others are subtype specific; c) there are genetic deletions at novel chromosomal regions; and d) several homozygous deletions have been noted. Our studies demonstrate the usefulness of continuous cell lines for detailed allelotyping, for comparing genetic abnormalities between SCLC and NSCLC, and for identifying homozygous deletions.

Cytogenetic abnormalities in an in situ ductal carcinoma and five prophylactically removed breasts from members of a family with hereditary breast cancer

Short-term cultures of tissue samples from three bilateral prophylactic mastectomies and one in situ ductal carcinoma from four women belonging to a family with hereditary breast cancer were cytogenetically analyzed. Clonal chromosome abnormalities were detected in five of the six prophylactically removed breasts, all of which had the histologic diagnosis epithelial hyperplasia without atypia, and in the in situ carcinoma. The same karyotypic imbalance, a loss of 3p12-14, was detected in the in situ carcinoma as well as in one of the hyperplasias, indicating that these bands may harbor a pathogenetically relevant gene in this breast cancer family. The finding of chromosome aberrations in clonal proportions in the prophylactically removed breasts indicates that a neoplastic process was already present, lending support to the view that prophylactic bilateral mastectomy in these high-risk individuals prevented the development of breast carcinoma.