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PubMed2004

Genetic counseling for hereditary pancreatitis--the role of molecular genetics testing for the cationic trypsinogen gene, cystic fibrosis and serine protease inhibitor Kazal type 1.

The importance of pretest information, using an accredited DNA laboratory and interpreting the genotype on behalf of the patient and their physicians is emphasized. Care with predictive testing and the strong encouragement to involve a specialist genetic counseling service is made. A similar approach to genetic testing should be used when children are involved. Because of the incomplete pickup of PRSS1 mutations, particularly of a limited mutation panel of R122H and N291 (perhaps with A16V), a diagnosis of HP cannot be ruled out by molecular genetic testing alone. The A16V mutation has a reduced penetrance, and its contribution to pancreatitis remains unclear. The advice to patients with genetic forms of pancreatitis is a strong encouragement to avoid smoking, to avoid alcohol, and to remain in contact with clinical and research groups for their follow-up and screening trials for early pancreatic cancer. The remaining issues are of how wide to cast the net of investigation in patients with unexplained pancreatitis, particularly looking for mutations in the CFTR and lower penetrance genes such as PSTI/SPINK1.

Algorithms↗

PubMed2001

Diverse clinical outcomes of eosinophilic patients with T-cell receptor gene rearrangements: the emerging diagnostic importance of molecular genetics testing.

Abnormal clones of clusters of differentiation (CD)3(-)CD4(+) or CD3(+)CD4(-)CD8(-) phenotypically abnormal lymphocytes have been identified in some patients who have the idiopathic hypereosinophilic syndrome. This report illustrates the disparate clinical courses of six eosinophilic patients with evidence of abnormal T-cell clones based on the finding of a T-cell receptor gene rearrangement. The data suggest that molecular genetics testing for T-cell receptor gene rearrangements should be included in the routine work-up of patients with idiopathic eosinophilia.

Adult↗

PubMed2006

[Thyroid carcinomas and Hirschsprung's disease--10-year experience with molecular genetic testing of the RET proto-oncogene].

In the last ten years, research has confirmed the role of the RET proto-oncogene in the pathogenesis of thyroid cancer such as medullary thyroid carcinoma (MTC) and papillary thyroid carcinoma (PTC), multiple endocrine neoplasia type 2 (MEN 2) and Hirschsprung's disease that can be associated with MTC or MEN 2. Through the use of molecular genetic testing, we are able to detect gene mutations and the course the disease might take can be predicted, thus enabling us to cure mutation carriers among the high-risk patients can at a very early, clinically asymptomatic stage of the disease; prophylactic total thyreoidectomy in said patients is recommended. At this juncture, there is extensive on-going research on the physiological role played by the RET proto-oncogene on the normal proliferation, differentiation and survival of the cell. Thanks to the new findings there are now possibilities of the theurapeutic use of gene therapy on an RET signaling cascade level in near future.

Carcinoma, Medullary↗

PubMed2002

A 39-bp deletion polymorphism in PTEN in African American individuals: implications for molecular diagnostic testing.

Germline mutations in the PTEN/MMAC1/TEP1 tumor suppressor gene cause Cowden syndrome (CS), a hereditary hamartoma-tumor syndrome with an increased risk of breast, thyroid, and endometrial cancers, and seemingly unrelated developmental disorders, such as Bannayan-Riley-Ruvalcaba (BRR) syndrome, Proteus, and Proteus-like syndromes. Data to date suggest that irrespective of the clinical presentation, the identification of a PTEN mutation should trigger medical management which includes cancer surveillance. Clinic-based molecular diagnostic testing for germline PTEN mutations has been available for at least 2 years. This study reports on the finding of a previously unobserved heterozygous alteration (IVS7-15-->53del39) found in an African American individual who had features of CS. Further investigation revealed that 12 of 42 (28.6%) African American controls, but not individuals of Caucasian or Japanese origin, also carried this heterozygous 39-bp deletion in PTEN. Due to its location immediately upstream of the splicing site of exon 8, this polymorphism could be mistaken for a deleterious mutation in the PTEN.

Base Sequence↗

PubMed2000

Test of molecular mode coupling theory for general rigid molecules

We report recent progress on the test of mode coupling theory for molecular liquids (MMCT) for molecules of arbitrary shape. The MMCT equations in the long time limit are solved for supercooled water including all molecular degrees of freedom. In contrast to our earlier treatment of water as a linear molecule, we find that the glass-transition temperature T(c) is overestimated by the theory as was found in the case of simple liquids. The nonergodicity parameters are calculated from the "full" set of MMCT equations truncated at l(co)=2. These results are compared (i) with the nonergodicity parameters from MMCT with l(co)=2 in the "dipole" approximation n=n(')=0 and the diagonalization approximation n=n(')=0, l=l(') and (ii) with the corresponding results from a MD simulation. This work supports the possibility that a reduction to the most prominent correlators may constitute a valid approximation for solving the MMCT equations for rigid molecules.

Journal Article↗

PubMed2005

Nevoid Basal Cell Carcinoma Syndrome in infants: improving diagnosis.

BACKGROUND: Diagnosis of Nevoid Basal Cell Carcinoma Syndrome (NBCCS) in infants may pose significant challenges to clinicians owing to its variable expressivity and age-related manifestations. METHODS: We report two paediatric cases of NBCCS who presented initially with a non-specific phenotype. RESULTS: In case 1, a diagnosis of NBCCS was possible only after the father was interviewed and found to present with two major criteria for the disease. Subsequent molecular testing confirmed the diagnosis. In case 2, molecular testing of the infant and his father had diagnostic value as neither satisfied fully the current diagnostic criteria for NBCCS. CONCLUSIONS: Presence of the few clinical manifestations of NBCCS that appear in infants, typically congenital malformations and skeletal abnormalities, should prompt clinicians to conduct in-person interviews with both parents. In general, paediatricians should refer both parents of infants who are suspected of having an inherited condition to clinical geneticists for expert examination, given the potential unreliability of reported medical history.

Basal Cell Nevus Syndrome↗

PubMed1997

Cytogenetic and Molecular Evaluation in Myelodysplastic Syndrome and in Acute and Chronic Leukemia.

BACKGROUND: The majority of the presently known nonrandom chromosome changes in hematologic malignancy were described during the 1970s and 1980s. The last 10 years have been devoted to the location of oncogenes and tumor suppressor genes altered as a consequence of those changes. New molecular methodology has helped speed this process, which has resulted in DNA sequencing of many of the genes involved, permitting molecular detection of abnormal clones. METHODS: This review examines the most common alteration-based subgroups of cytogenetics and molecular genetics in hematologic disorders with the exclusion of lymphoma. Prognosis has been updated to reflect improving treatment protocols. RESULTS: The versatility of cytogenetics for delineating genetic changes is difficult to match by molecular testing. Once a clonal anomaly is identified, molecular methodology can detect residual disease with far greater sensitivity than cytogenetics, but relies on translocation junction targets that exclude clones characterized by deletion or trisomy. CONCLUSIONS: Cytogenetic and molecular testing offers independent diagnostic and prognostic evaluation for most patients with hematologic malignancy.

Journal Article↗

PubMed2001

Molecular genetic testing for neuronal ceroid lipofuscinoses.

Eight different NCL forms have been recognized to be encoded by genes CLN1-8. CLN1,2,3,5,and 8 have been cloned, and at least 85 mutations have been detected. Molecular technology can now be applied to genetic testing for NCLs; testing is now available in clinic diagnostic and research laboratories for CLN genes that have been cloned. Molecular genetic testing makes it possible not only to confirm clinical and pathological diagnoses but also to offer pre-symptom diagnosis and carrier screening for NCL families. In addition, DNA-based mutation analysis may predict prenatal outcome more accurately for pregnant women in NCL families.

Cloning, Molecular↗

PubMed1996

Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies.

The statistical properties of the paralinear and LogDet distances under nonstationary nucleotide frequencies were studied. First, we developed formulas for correcting the estimation biases of the paralinear and LogDet distances, i.e., the bias-corrected distance is estimated by dc = d - 2var(d), where d and var(d) are the estimated distance and sampling variance, respectively. The performances of these formulas and the formulas for sampling variances were examined by computer simulation. Second, we developed a method for estimating the variance-covariance matrix of paralinear distances, so that statistical tests of DNA phylogenies can be conducted in the nonstationary case. Third, a new LogDet-based method for testing the molecular clock hypothesis was developed under nonstationary nucleotide frequencies.

Analysis of Variance↗

PubMed2004

[Susceptibility testing and molecular epidemiology of clinical strains of Bordetella pertussis isolated in Japan from 2001 to 2002].

We determined antimicrobial susceptibilities and analyzed molecular epidemiology of 26 strains of Bordetella pertussis clinically isolated and then performed pulsed-field gel electrophoresis (PFGE) in Japan (Japanese Pertussis Surveillance Group Participants), from 2001 to 2002. The MICs of erythromycin, clindamycin, tetracyclines, fluoroquinorones, trimethoprim-sulfamethoxazole and rifampicin of all isolates against these showed 1 microgram/ml or less. Sparfloxacin is the most potent agent, of which the MICs showed 0.008-0.016 microgram/ml. Results of DNA fingerprinting by pulsed-field gel electrophoresis (PFGE) differentiated three types (Type I; 11 strains (42%), type II; 14 strains (54%) and type III; 1 strains (4%)). However, no relation between regions and identical PFGE patterns was found in this study. Further, surveillance of the antimicrobial susceptibilities and molecular epidemiology of B. pertussis will be required.

Anti-Bacterial Agents↗

PubMed1996

A 'litmus test' for molecular recognition using artificial membranes.

BACKGROUND: Sensitive and selective molecular recognition is important throughout biology. Certain organisms and toxins use specific binding at the cell surface as a first step towards invasion. A new series of biomolecular materials, with novel optical and interfacial properties, have been designed to sense molecular recognition events. These polymers, the diacetylenic lipids, have previously been shown to undergo chromatic transitions in response to virus binding to the surface of the material. RESULTS: Gangliosides that specifically bind cholera toxin, heat-labile Escherichia coli enterotoxin and botulinum neurotoxin were incorporated into a matrix of diacetylenic lipids, 5-10% of which were derivatized with sialic acid. The lipids were self-assembled into Langmuir-Blodgett layers and polymerized with ultraviolet irradiation, yielding a polydiacetylene membrane with a characteristic blue color into which the ganglioside is non-covalently incorporated. When toxin is added, the polymerized membrane turns red. The response is specific and selective, and can be quantified by visible absorption spectrophotometry. CONCLUSIONS: Polydiacetylenic lipid membranes offer a general 'litmus test' for molecular recognition at the surface of a membrane. A concentration of 20 ppm of protein could be detected using polymerized thin films. The speed, sensitivity and simplicity of the design offers a new and general approach towards the direct colorimetric detection of a variety of different molecules.

Biosensing Techniques↗

PubMed2003

How Bayes tests of molecular phylogenies compare with frequentist approaches.

MOTIVATION: The desire to compare molecular phylogenies has stimulated the design of numerous tests. Most of these tests are formulated in a frequentist framework, and it is not known how they compare with Bayes procedures. I propose here two new Bayes tests that either compare pairs of trees (Bayes hypothesis test, BHT), or test each tree against an average of the trees included in the analysis (Bayes significance test, BST). RESULTS: The algorithm, based on a standard Metropolis-Hastings sampler, integrates nuisance parameters out and estimates the probability of the data under each topology. These quantities are used to estimate Bayes factors for composite vs. composite hypotheses. Based on two data sets, the BHT and BST are shown to construct similar confidence sets to the bootstrap and the Shimodaira Hasegawa test, respectively. This suggests that the known difference among previous tests is mainly due to the null hypothesis considered.

Algorithms↗

PubMed1999

Molecular genetic testing from paraffin-embedded tissue distinguishes nonmolar hydropic abortion from hydatidiform mole.

BACKGROUND: Diagnosis of hydatidiform mole by histology and ploidy analysis is limited by overlap of criteria for nonmolar hydropic abortion, complete mole, and partial mole. With early presentation, diagnosis is difficult due to limited tissue and lack of clinical features. Accurate diagnosis of these entities is important for both prognosis and patient management. We assessed a polymerase chain reaction (PCR) assay for polymorphic short tandem repeats (STR) for discrimination between nonmolar hydropic abortion, complete mole, and partial mole based on the genetic composition of molar pregnancies. METHODS: Seventeen cases of products of conception (POC) diagnosed by histology and flow cytometry ploidy analysis were studied retrospectively. PCR was performed using maternal and chorionic villus DNA extracted from microdissected, formalin-fixed, paraffin-embedded tissue sections. Allelic patterns for up to eight well-characterized polymorphic STR loci were determined using the GenePrint Fluorescent STR System (Promega Corporation, Madison, WI). The presence of three villus alleles at a single locus was interpreted as partial mole. Detection of only one allele in the villi, different from all maternal allele(s) at the same locus, was interpreted as a complete mole. RESULTS: This technique identified eight complete moles previously diagnosed as complete mole (3), hydatidiform mole, otherwise unspecified (1), hydropic villi (2), hydropic villi versus partial mole (1), and partial mole (1). The diagnoses of five partial moles by the molecular assay were consistent with the diagnoses by histology and flow cytometry. One nonmolar gestation was identified, which had been diagnosed previously as hydropic villi. In three cases, maternal DNA amplification was insufficient for definitive diagnosis. CONCLUSION: Molecular genetic testing of POC from paraffin-embedded tissue accurately distinguishes complete mole, partial mole, and nonmolar hydropic abortion. Identification of triploidy by flow cytometry can confirm a histological impression of partial mole. Histological and ploidy analysis of POC results in underdiagnosis of complete moles.

Abortion, Spontaneous↗

PubMed2000

Molecular diagnostic tests in the diagnosis and management of thyroid carcinoma.

The application of molecular analysis of gene expression to clinical tissue samples represents one of the most exciting new areas in "translational" thyroid cancer research. Current data suggest that molecular diagnostic assays may improve the sensitivity and accuracy of fine needle aspiration of thyroid nodules, fine needle aspiration of metastases, and detection of recurrent disease in peripheral blood samples. It is likely that at least some of these tests will become useful adjuncts in the diagnostic armamentarium of clinical endocrinologists in the future.

Biomarkers, Tumor↗

PubMed1988

Imaging of the stomach, and localization of the stomach meridian & its acupuncture points in a human cadaver by the use of the indirect "Bi-Digital O-Ring Test Imaging Technique".

Since 1984, using the "Bi-Digital O-Ring Test (Molecular Identification, Localization and) Imaging Technique" originally developed by Y. Omura, the imaging of the outline of normal and abnormal internal organs has been successfully applied for clinical diagnosis and evaluation of therapeutic effects, without the use of expensive imaging instrumentation. Not only has it become possible to non-invasively image each internal organ and localize specific malignant tumors of specific internal organs, as well as neurotransmitters, but it has also recently become possible to demonstrate the presence and exact locations of the meridians corresponding to specific internal organs and their acupuncture points along the meridians through the use of either the Direct or Indirect "Bi-Digital O-Ring Test (Molecular Identification, Localization and) Imaging Techniques" while holding a microscopic slide of the specific human internal organ tissue. However, very little information was available to demonstrate the presence of the meridians and their acupuncture points in a human cadaver. In this study, we were able to demonstrate by use of the Indirect "Bi-Digital O-Ring Test (Molecular Identification, Localization and) Imaging Technique" the presence of meridians corresponding to specific internal organs and acupuncture points on the meridians, all of which were nearly identical to those found in a living human. For example, the authors found that the stomach meridian at both ends of one of the most well-known acupuncture points, Stomach 36, is located within 1 mm of the surface of the skin, and the average diameter of the meridian is less than 1 mm. Stomach 36 in this particular cadaver had a round shape with a diameter of approximately 1.8 cm at the skin surface. The acupuncture point, St. 36, in this cadaver at the skin surface was round in shape and extended to the deepest underlying muscle layer of the tibialis anterior muscle, in three dimensions. In spite of the fact that the Indirect Bi-Digital O-Ring Test Imaging Technique showed a distinct pathway for the stomach meridian and the location of St. 36, there was no apparent difference to the naked eye between the meridian and the surrounding non-meridian tissue, nor between St. 36 and surrounding non-acupuncture point area. However, there seems to be a more dense connective tissue network between the skin layer and the fascia on the muscle tissue at the acupuncture point, as compared with the surrounding non-acupuncture point area.(ABSTRACT TRUNCATED AT 400 WORDS)

Acupuncture Therapy↗

PubMed2000

Multiple molecular marker testing (p53, C-Ki-ras, c-erbB-2) improves estimation of prognosis in potentially curative resected non-small cell lung cancer.

A prospective study was performed in patients with non-small cell lung cancer (NSCLC) to evaluate the prognostic importance of multiple molecular marker (p53, c-Ki-ras, c-erbB-2) testing. 103 patients with potentially curative resections (RO resection) for NSCLC in histopathological stages I-IIIA were included. SSCP analysis and DNA sequencing for p53 and c-Ki-ras genes were performed on paired tumour and normal lung tissue samples and immunohistochemistry (c-erbB-2) was done on frozen tissue sections with a specific anti-c-erbB-2 monoclonal antibody. 46/103 (44.6%) NSCLC showed p53 mutations and 17/103 (16.5%) c-Ki-ras mutations including 12/37 (32.4%) adenocarcinomas. Overexpression of c-erbB-2 (p185) was detected in 56/103 (54.4%) tumours. 24/103 (23.3%) NSCLC were negative for alterations in all 3 parameters (c-Ki-ras, p53 and p185) whereas 79/103 (76.7%) were positive for at least one of the 3 parameters. In a regression model including a multiple molecular marker parameter (negative for all 3 markers versus positive for at least one marker), histopathological stage (P<0.00001), respectively the pT (P<0.01) and pN (P<0.00001) categories and the multiple molecular marker parameter (P<0.01) were of significant prognostic importance. This study demonstrates that testing 3 molecular markers (c-Ki-ras, p53 and c-erbB-2) improves estimation of prognosis compared to single marker testing and appears to define low (82.6%+/-7.9% 5-year survival) and high risk (40.2%+/-5.5% 5-year survival) groups for treatment failure in potentially curative (RO) resected NSCLC.

Adult↗

PubMed2004

Molecular analysis of patients with synostotic frontal plagiocephaly (unilateral coronal synostosis).

Mutations in genes known to be responsible for most of the recognizable syndromes associated with bilateral coronal synostosis can be detected by molecular testing. The genetic alterations that could cause unilateral coronal synostosis are more elusive. It is recognized that FGFR and TWIST mutations can give rise to either bilateral or unilateral coronal synostosis, even in the same family. The authors undertook a prospective study of patients presenting with synostotic frontal plagiocephaly (unilateral coronal synostosis) to Children's Hospital Boston during the period from 1997 to 2000. Mutational analysis was performed on all patients and on selected parents whenever familial transmission was suspected. Intraoperative anthropometry was used in an effort to differentiate those patients in whom a mutation was detected from those in whom it was not. The anthropometric measures included bilateral sagittal orbital-globe distance, inter medial canthal distance, and nasal angulation. Macrocephaly and palpebral angulation were also considered possible determinants. There was a 2:1 female preponderance in 47 patients with synostotic frontal plagiocephaly. Mutations were found in eight of 47 patients: two patients with different single-amino-acid changes in FGFR2, three patients with FGFR3 Pro250Arg, and three patients with TWIST mutations. Another patient had craniofrontonasal syndrome for which a causative locus has been mapped to chromosome X, although molecular testing is not yet available. Two features were strongly associated with a detectable mutation in patients with synostotic frontal plagiocephaly: asymmetrical brachycephaly (retrusion of both supraorbital rims) and orbital hypertelorism. Other abnormalities in the craniofacial region and extremities were clues to a particular mutation in FGFR2, FGFR3, TWIST, or the X-linked mutation. Neither macrocephaly nor degree of nasal angulation nor relative vertical position of the lateral canthi correlated with mutational detection. An additional four patients in this study had either unilateral or bilateral coronal synostosis in an immediate relative and had anthropometric findings that predicted a mutation, and yet no genetic alteration was found. This suggests either that the authors' screening methods were not sufficiently sensitive or that perhaps there are other unknown pathogenic loci. Nevertheless, molecular testing is recommended for infants who have unilateral coronal synostosis, particularly if there are the anthropometric findings highlighted in this study or an otherwise suspicious feature in the child or a parent. Infants with either an identified or a suspected mutation usually need bilateral asymmetric advancement of the bandeau and may be more likely to require frontal revision in childhood.

Adult↗

PubMedDate not supplied

The ethical, legal and psychosocial challenges of genetic testing: implications for primary medical care.

Recent advances in genetic information and technology have led to an explosion in molecular testing for mutations that cause human disease. Test results are likely to improve medical management and/or help individuals make important life and reproductive decisions. Unlike other laboratory testing, unique complexities and challenging psychosocial, legal and financial ramifications often accompany genetic tests. Some of the challenges associated with molecular testing and examples illustrating potential ethical, psychosocial and legal complexities are presented here.

Adult↗