A high-resolution map of segmental DNA copy number variation in the mouse genome

Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.

Identification of candidate alkylator-induced cancer susceptibility genes by whole genome scanning in mice

Secondary malignancies are a serious adverse consequence of alkylator chemotherapy. The risk of developing an alkylator-associated malignancy is influenced by genetic background, although the relevant genetic factors are poorly understood. To screen for novel susceptibility factors, we established a mouse model of alkylator-induced malignancy. We exposed mice from 20 inbred strains to the prototypical alkylating agent, N-nitroso-N-ethylurea (ENU). ENU was a potent carcinogen in many of the strains tested, inducing 140 tumors in 240 ENU-treated mice (66% incidence of at least one tumor in evaluable mice), compared with a background incidence of 8% spontaneous tumors in 240 strain-, age-, and sex-matched control mice (relative risk, 8.4; P < 0.0001). A wide variety of tumor histologies were noted, including epithelial carcinomas, soft tissue sarcomas, and hematopoietic tumors. Cancer susceptibility was a heritable trait for the most common tumor types, lung adenocarcinoma (H(2) = 0.25), T cell lymphoma (H(2) = 0.19), and myeloid malignancies (H(2) = 0.10). Quantitative trait locus mapping identified regions on chromosomes 3, 6, 9, and 15 containing candidate genes associated with lung adenoma, lung carcinoma, and lymphoma susceptibility. This novel mouse model recapitulates many features of human alkylator-associated cancer and supports the hypothesis that susceptibility to this syndrome is influenced by inherited polymorphisms that could be used to make informed clinical treatment decisions.

DNA sequence variation and haplotype structure of the ICAM1 and TNF genes in 12 ethnic groups of India reveal patterns of importance in designing association studies

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non-synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF-376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between-population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case-control association studies.

Insertion/Deletion Polymorphisms in Tribal Populations of Southern India and Their Possible Evolutionary Implications

India has the unique distinction of having perhaps the largest diversities, both biological and cultural. The Nilgiri Hills of southern India, a home for several tribal pockets representing different genetic isolates, provides a genetic wealth to understand human evolution. We have analyzed eight widely distributed polymorphic insertion/deletion loci (AluAPO, AluACE, AluDI, AluPLAT, AluPV92, AluFXIIIB, CD4 del and mtNUC) in 250 unrelated individuals from five tribal populations (Badaga, Irula, Kota, Kurumba, and Toda). All loci were highly polymorphic except the CD4 del locus, at which the deletion allele was fixed in Kotas and Kurumbas. The levels of average heterozygosities were found to be high in all the populations. In most populations, they were also higher than those predicted by the island model of population structure. The gene diversity (GST = 8.3%) was found to be higher than that in populations of most global regions with the exception of Africa. It is clear from the present study that drift effects could have accentuated the process of genetic differentiation of the tribal populations. The possibility of an early demographic expansion of modern humans within south India also cannot be ruled out.

An anticlastogenic in vivo micronucleus assay for tea

Common use of antimutagens and anticarcinogens in everyday life is an effective measure for preventing human cancer and genetic diseases. Antioxidant properties of tea have vast potential as protective agents against diverse toxic effects. The present study was aimed to evaluate the role of aqueous clonal tea extracts (green tea, oolong tea and black tea) in modulating the genotoxic damage induced by cyclophosphamide (CP), a commonly used chemotherapeutic drug and a well-known mutagen and clastogen. All the three tea extracts at 1 and 2% concentration did not increase the frequency of micronucleated polychromatic erythrocytes (MPE) in bone marrow cells of mice when administered individually. The tea extracts decreased the micronuclei (MN) induced by CP. Therefore, regular intake of tea may improve the antioxidant status in in vivo and thereby reduce the risk of cancer and coronary heart disease.

Trace metal concentration in scalp hair of occupationally exposed autodrivers

The concentrations of Cr, Pb, Zn, Cu, Ni and Cd were analyzed by Atomic Absorption Spectrophotometer in the scalp hair of professional male autodrivers who are occupationally exposed to the vehicular/industrial pollutants in the industrial city of Coimbatore, Tamil Nadu. The unwashed hair samples when compared with the washed hair showed a significantly higher levels of Cr, Zn and Pb. The correlation coefficient showed a strong mutual dependence on the scalp hair of the exposed individuals and no correlation was found among the trace metals except for Ni-Pb and Ni-Cd. The results in general showed a positive exogenous contribution of all the analyzed industrial trace metals. The drivers who are occupationally exposed to vehicular/industrial pollution are at risk.

Proton MR spectroscopic imaging predicts lesion progression on MRI in X-linked adrenoleukodystrophy

BACKGROUND

The phenotypic expression of X-linked adrenoleukodystrophy (X-ALD) ranges from the rapidly progressive childhood cerebral form to the milder adrenomyeloneuropathy in adults. It is not possible to predict phenotype by mutation analysis or biochemical assays. Multislice proton MRS imaging (MRSI) has previously detected more extensive brain abnormalities in X-ALD than conventional MRI, which has been suggested to predict impending demyelination. However, the significance of these changes is unclear.

OBJECTIVE

The purpose of this study was to determine the long-term sensitivity and specificity of MRSI for disease progression in X-ALD.

METHODS

Twenty-five patients with X-ALD were investigated (average age, 15 years; range, 2-43 years) with MRI and proton MRSI at baseline and follow-up MRI over a mean period of 3.5 years. Eight patients had normal MRI findings at baseline and on follow-up (noncerebral group), 11 had abnormal MRI at baseline and no change on follow-up (cerebral nonprogressive group), and 6 had progressive MRI abnormalities (cerebral progressive group). On MRSI, voxels were analyzed in the normal MRI-appearing perilesional white matter, or in the corresponding area in the noncerebral group.

RESULTS

The concentration ratio of N-acetylaspartate (NAA) to choline was the most sensitive indicator of disease progression. The average NAA/choline ratio was 5.99 for the noncerebral group, 5.75 for the cerebral nonprogressive group, and 3.74 for the cerebral progressive group (p = 0.002). At a cut-off point of 5.0, the NAA/choline ratio predicted disease progression in all patients with six cerebral progressive disease (sensitivity 100%). The specificity was 83%, the positive predictive value was 66%, and the negative predictive value was 100%.

CONCLUSIONS

Multislice proton MRS imaging is able to identify impending or beginning degeneration in white matter that still appears normal on conventional MRI. Multislice proton MRSI may be a suitable technique for the prediction of lesion progression on MRI in X-linked adrenoleukodystrophy.

Cognitive impairment in alcoholic and nonalcoholic cirrhotic patients

Cognitive impairment is common in patients with advanced liver disease. It has been suggested that patients with alcoholic liver disease (ALD) have more impaired cognition than nonalcoholics. The objective of this study was to characterize any differences in cognitive functions between alcoholic cirrhotic patients and non-alcoholic cirrhotic patients of similar age, education, and severity of liver disease. We assessed cognitive functions in 117 patients with alcoholic cirrhosis and 163 patients with nonalcoholic cirrhosis using a brief battery of neuropsychological tests. In addition, all patients had standard psychiatric examinations to assess the effect of the disease severity, alcoholism, anxiety, and depression on the test scores. The study showed a higher proportion of patients with cognitive impairment in the alcoholic group. Alcoholics performed poorly in tests of memory and motor speed compared with nonalcoholics, despite similar premorbid IQ and education. Because patients with alcoholic cirrhosis had more severe liver disease (Child-Pugh score 8.5 +/- 2.2 vs. 7.6 +/- 2.2, P =.03) than nonalcoholics, the results were reanalyzed after adjusting for the linear effects of Child-Pugh score on cognitive test scores. We also used two-way analysis of variance to examine the interaction between Child class and alcoholism. Finally, the test scores were compared within each Child class. These analyses revealed no primary or interaction effect of alcoholism and confirmed that the differences in the test scores observed in alcoholics reflect the greater severity of their liver disease. The severity of cognitive impairment is similar in both alcoholic and non-alcoholic cirrhotic patients when adjusted for the severity of liver disease.

Liver transplantation for alcoholic liver disease

Orthotopic liver transplantation (OLT) for individuals with alcoholic liver disease (ALD) remains controversial. This review was designed to evaluate the survival, recidivism, and rehabilitation of the alcoholic liver transplant recipient in a single transplant center.

METHODS

Between 10/86 and 11/92 203 liver transplants were performed in 179 patients. In 42 patients (23%) the primary etiologic diagnosis was ALD (36 males, 6 females, median age 47 yr). All ALD patients were evaluated preoperatively by social service, psychiatry, and medical psychology, in addition to hepatology and transplant surgery. A minimum abstinence period of 3-6 months was encouraged, although exceptions were made for cases of extreme medical urgency in which a good prognosis for abstinence was predicted.

RESULTS

In OLT recipients with ALD, actuarial survival at 1, 2, and 3 yr was 74%, 71%, and 71%, respectively, compared to 71%, 71%, and 69% for all OLT recipients. One- and two-year survival was 85% in the most recently transplanted 86 patients, 20 of whom (23%) had ALD with 1- and 2-yr survival of 84% (N.S.). Recidivism was monitored postoperatively by interviews with the patient and family, supplemented by random urine and serum toxicology. Of the 29 survivors, 2 (7%) returned temporarily to alcohol use but are presently abstinent. Although none of the ALD patients in this study was able to work prior to OLT, 76% of the survivors at least 4 months post-transplantation were employed.

CONCLUSIONS

Although our experience is small, our results suggest that OLT is appropriate therapy for carefully selected patients with end-stage liver failure due to ALD. The multi-disciplinary approach to preoperative evaluation of the alcoholic liver transplant candidate is effective in determining those patients committed to abstinence after a successful transplant.

Cognitive and brain magnetic resonance imaging findings in adrenomyeloneuropathy

Neuropsychological functioning and brain magnetic resonance imaging (MRI) were evaluated in 84 men with adrenomyeloneuropathy (AMN). MRI was normal in 61%, the "pure AMN" group, while 39%, the "cerebral AMN" group, showed brain white matter abnormalities. Except for mild deficits in psychomotor speed and visual memory, neuropsychological function was normal in pure AMN. Most patients with cerebral AMN had normal IQ and language but evidenced impaired psychomotor speed, spatial cognition, memory, and executive functions. Patients with MRI evidence of very severe cerebral disease had global and language impairment as well, and deficits in all patients were highly correlated with degree of brain MRI involvement.

Prognostic value of psychological testing in patients undergoing spinal cord stimulation: a prospective study

OBJECTIVE

Associations between psychological and physical states are understood to exist, and the development of standardized psychological tests has allowed quantitative evaluation of this relationship. We tested whether associations exist between psychological test instruments and patients selected for therapeutic trials of spinal cord stimulation (SCS) for chronic, intractable pain.

METHODS

Fifty-eight patients selected for SCS were tested prospectively with a battery of standardized psychological tests: Minnesota Multiphasic Personality Inventory with Wiggins content scales, Symptom Check List-90, and Derogatis Affects Balance Scale. Associations between treatment outcomes and preoperative test scores and clinical variables were tested by univariate and multivariate statistical analyses, in which the dependent variables were as follows: 1) the outcome of a therapeutic trial of stimulation (whether the patient derived sufficient reported pain relief with a temporary electrode to proceed with a permanent implant), and 2) long-term outcome of treatment with the permanent implant, as determined by disinterested third-party interview.

RESULTS

Significant associations (P < or = 0.01) were observed between the outcome of the therapeutic trial of stimulation and psychological test results; patients with low "anxiety" scores on the Derogatis Affects Balance Scale and with high "organic symptoms" scores on the Wiggins test were significantly more likely to proceed to permanent implants, as determined by multivariate statistical models. There was an elevation in the Minnesota Multiphasic Personality Inventory hypochondriasis scale in these patients by univariate (P = 0.02), but not by multivariate, models. The multivariate model also identified young age, reproduction of leg pain by straight leg raising, and bilateral leg pain as favorable prognostic factors. The only association with favorable long-term outcome of implantation of a permanent device, by univariate analysis, was an elevated "joy" score on the Derogatis Affects Balance Scale. Multivariate analysis revealed no statistically significant predictors of long-term outcome.

CONCLUSION

Because our study population was selected on the basis of recognized prognostic factors and long clinical experience, it may not be possible to generalize our findings to the overall pain clinic referral population. In the subpopulation we have chosen for SCS trials, psychological testing is of modest value and explains little of the observed variance in outcome. We find little evidence for selecting patients for SCS on the basis of psychological testing. Because self-reported outcome measures may themselves reflect the patient's psychological state, these findings should be considered carefully, in overall clinical context. A prospective study with additional objective outcome measures is underway, which will address some of these issues.

Increased signals seen in globus pallidus in T1-weighted magnetic resonance imaging in cirrhotics are not suggestive of chronic hepatic encephalopathy

Increased, symmetrical signals of varying intensity in the globus pallidi on T1-weighted (T1W) images, without corresponding signals on T2-weighted (T2W) images, have been reported previously in chronic hepatic failure. It has been suggested that these signals are characteristic of chronic hepatic encephalopathy. To test this hypothesis, we evaluated the relationship of magnetic resonance imaging (MRI) abnormalities with ammonia, albumin, bilirubin, prothrombin time, ascites, clinical encephalopathy, and neuropsychological tests in 46 patients (16 with alcohol-induced cirrhosis and 30 with non-alcohol-induced cirrhosis). T1W signal and cortical atrophy were graded by a neuroradiologist in a blinded fashion. Eleven patients had no T1W signal, 18 had minimal T1W signal, and 17 had high T1W signal. Twenty-five patients had no cortical atrophy, 14 had mild atrophy, and 7 had moderate atrophy. Cortical atrophy was noted more commonly in patients with alcohol-induced liver disease. The neuropsychological tests correlated significantly with albumin, prothrombin time, Child-Pugh's score, clinical encephalopathy, and ammonia. T1W signal and cortical atrophy did not correlate with the neuropsychological tests, clinical encephalopathy, ascites, albumin, prothrombin time, ammonia, or Child-Pugh's score. Patients with high T1W signal showed significant correlation with bilirubin (P < .005). This study suggests that globus pallidus signal in T1W images observed in liver disease are not indicators of chronic hepatic encephalopathy as previously assumed.

MR findings in adult-onset adrenoleukodystrophy

PURPOSE

To describe the MR findings of brain and spinal cord in adult-onset adrenoleukodystrophy.

METHODS

One hundred sixty-four adult patients ranging from 19 to 74 years of age (119 men and 45 women) with clinically and biochemically proved adrenoleukodystrophy underwent MR of the brain. In 30 patients the spinal cord also was evaluated with MR.

RESULTS

The brain MR findings were abnormal in 54 of 119 males and in 9 of 45 female heterozygotes and consisted of varying degrees of demyelination of the cerebral white matter in 40 patients, corpus callosum in 25 patients, corticospinal tracts in 46 patients, visual tracts in 31 patients, and auditory tracts in 18 patients. The thoracic spinal cord showed diffuse atrophy in 18 of 20 men and in 8 of 10 women.

CONCLUSION

It is important to recognize the MR findings of adult-onset adrenoleukodystrophy, because not uncommonly the clinical and MR findings of adrenoleukodystrophy are misdiagnosed as multiple sclerosis, olivopontocerebellar or spinocerebellar atrophy, amyotrophic lateral sclerosis, or dementia. Analysis of the MR findings and correlation of the clinical findings has permitted a tentative subdivision of adult-onset adrenoleukodystrophy population into four subtypes that appear to differ in respect to prognosis and possibly pathogenesis. MR evaluation of the brain in adrenoleukodystrophy also is helpful in patient selection for experimental therapy, which is most effective if offered in the early stage of the disease.

Cognitive impairment in adult-onset adrenoleukodystrophy

Adrenoleukodystrophy (ALD) is a progressive X-linked disorder that produces pathological changes, mainly in the adrenal cortex and the white matter of the central nervous system. The main biochemical abnormality is the accumulation of saturated unbranched fatty acids with a chain length of 24 or more, referred to as very-long-chain fatty acids (VLCFA). Affected children develop large zones of demyelination associated with perivascular lymphoctyic infiltrations resembling those seen in multiple sclerosis. Adults show a more chronic form of the disease, referred to as adrenomyeloneuropathy (AMN). AMN mainly involves the spinal cord ad peripheral nerves, although the cerebral hemispheres may also be affected. Approximately 15% of female carriers have nervous-system involvement that resembles AMN. It is well known that ALD may initially appear as a psychiatric disorder. In the present study, we have assessed the prevalence of cognitive impairment in a group of AMN patients and neurologically symptomatic ALD heterozygotes initially presenting primarily physical complaints. Sixty percent of these patients demonstrated significant neuropsychological impairment, most commonly a pattern of spared and impaired functions typical of a subcortical dementia. We suggest that this progressive cognitive impairment may underlie other behavioral deficits, affirming the significance of the psychological features of this genetically determined disorder.