A genetic map of the mouse with 4,006 simple sequence length polymorphisms.

We have constructed a genetic map of the mouse genome containing 4,006 simple sequence length polymorphisms (SSLPs). The map provides an average spacing of 0.35 centiMorgans (cM) between markers, corresponding to about 750 kb. Approximately 90% of the genome lies within 1.1 cM of a marker and 99% lies within 2.2 cM. The markers have an average polymorphism rate of 50% in crosses between laboratory strains. The markers are distributed in a relatively uniform fashion across the genome, although some deviations from randomness can be detected. In particular, there is a significant underrepresentation of markers on the X chromosome. This map represents the two-thirds point toward our goal of developing a mouse genetic map containing 6,000 SSLPs.

Radiation hybrid map of the mouse genome.

Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. The construction of a comprehensive RH map for the human genome has resulted in gene maps reflecting the location of more than 30,000 human genes. Here we report the first comprehensive RH map of the mouse genome. The map contains 2,486 loci screened against an RH panel of 93 cell lines. Most loci (93%) are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps. We performed RH mapping by a new and efficient approach in which we replaced traditional gel- or hybridization-based assays by a homogeneous 5'-nuclease assays involving a single common probe for all genetic markers. The map provides essentially complete connectivity and coverage across the genome, and good resolution for ordering loci, with 1 centiRay (cR) corresponding to an average of approximately 100 kb. The RH map, together with an accompanying World-Wide Web server, makes it possible for any investigator to rapidly localize sequences in the mouse genome. Together with the previously constructed genetic map and a YAC-based physical map reported in a companion paper, the fundamental maps required for mouse genomics are now available.

A radiation hybrid map of mouse genes.

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome.

A YAC-based physical map of the mouse genome.

A physical map of the mouse genome is an essential tool for both positional cloning and genomic sequencing in this key model system for biomedical research. Indeed, the construction of a mouse physical map with markers spaced at an average interval of 300 kb is one of the stated goals of the Human Genome Project. Here we report the results of a project at the Whitehead Institute/MIT Center for Genome Research to construct such a physical map of the mouse. We built the map by screening sequenced-tagged sites (STSs) against a large-insert yeast artificial chromosome (YAC) library and then integrating the STS-content information with a dense genetic map. The integrated map shows the location of 9,787 loci, providing landmarks with an average spacing of approximately 300 kb and affording YAC coverage of approximately 92% of the mouse genome. We also report the results of a project at the MRC UK Mouse Genome Centre targeted at chromosome X. The project produced a YAC-based map containing 619 loci (with 121 loci in common with the Whitehead map and 498 additional loci), providing especially dense coverage of this sex chromosome. The YAC-based physical map directly facilitates positional cloning of mouse mutations by providing ready access to most of the genome. More generally, use of this map in addition to a newly constructed radiation hybrid (RH) map provides a comprehensive framework for mouse genomic studies.

A genetic linkage map of the mouse: current applications and future prospects.

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism.

Genetic susceptibility to Leishmania: IL-12 responsiveness in TH1 cell development.

The genetic background of T lymphocytes influences development of the T helper (TH) phenotype, resulting in either resistance or susceptibility of certain mouse strains to pathogens such as Leishmania major. With an in vitro model system, a difference in maintenance of responsiveness of T cells to interleukin-12 (IL-12) was detected between BALB/c and B10.D2 mice. Although naive T cells from both strains initially responded to IL-12, BALB/c T cells lost IL-12 responsiveness after stimulation with antigen in vitro, even when cocultured with B10.D2 T cells. Thus, susceptibility of BALB/c mice to infection with L. major may derive from the loss of the ability to generate IL-12-induced TH1 responses rather than from an IL-4-induced TH2 response.

Measuring brain volume by MR imaging: impact of measurement precision and natural variation on sample size requirements.

BACKGROUND AND PURPOSE: To determine the sample size needed to provide adequate statistical power in studies of brain volume by MR imaging, we examined the precision and variability of measurements in healthy controls. MATERIALS AND METHODS: A cohort of 52 people (mean age, 25.1 years) was examined at weeks 0 and 12 at 1.5 T. We used an axial multisection T1-weighted sequence and a contiguous proton-attenuation/T2-weighted sequence. Data were registered to a probabilistic brain atlas, and an automated atlas-based program was used to segment brain tissue by type and by lobe. We assumed that there were no changes in volume because there were no intervening neurologic events. Sample sizes required to yield 80% statistical power in detecting a significant difference in volume were calculated for various experimental designs, assuming a patient-control volume difference of 5% or 2%. RESULTS: The precision of most measurements was excellent, but required sample sizes were larger than anticipated. If the goal was to detect a 5% difference in whole brain volume in a 2-sample cross-sectional study, the required sample was 73 patients and 73 controls because brain volume varies between individuals in a way that is not informative about disease effects. For a similar 2-sample longitudinal study, the required sample size was just 5 patients and 5 controls. CONCLUSIONS: Our results argue strongly for longitudinal studies in preference to cross-sectional studies, especially as research budgets decline. Our findings also suggest that there may be more uncertainty than expected in published MR imaging brain volume studies.

Response of solid tumors to chemotherapy monitored by in vivo 31P nuclear magnetic resonance spectroscopy: a review.

In vivo 31P nuclear magnetic resonance (MR) spectroscopy has shown great promise as a tool for cancer research and the clinical management of solid tumors. It is now possible in some cases to integrate MR spectroscopy with routine MR imaging of the cancer patient, so that tissue identified as tumor on an MR image can be examined biochemically and monitored following treatment. Alterations have been observed in the phosphorus MR spectra of patient tumors after treatment, but the causes and consequences of these alterations are poorly understood. Here we review data obtained from experimental animal tumor models treated with chemotherapy in order to gain insight into the biological events reflected in MR spectroscopic changes, and to determine what information the spectra provide about the success or failure of therapeutic interventions. An attempt is made to relate these experimental findings to the cancer clinic and to analyze the contributions of MR spectroscopy to the understanding of tumor biology.

Response of radiation-induced fibrosarcoma-1 in mice to cyclophosphamide monitored by in vivo 31P nuclear magnetic resonance spectroscopy.

In vivo 31P nuclear magnetic resonance spectroscopy has been used to examine the RIF-1 fibrosarcoma in mice during untreated growth and following chemotherapy with cyclophosphamide. Levels of inorganic phosphate increase relative to phosphocreatine or nucleoside triphosphates during early untreated growth. After the tumor reaches a volume of approximately 1 g, no further decrease in energy level is observed. Following treatment with cyclophosphamide, tumor phosphorus metabolite ratios and pH are significantly altered, compared to untreated age-matched controls. During the growth delay period following chemotherapy there is a significant reduction in the ratio of inorganic phosphate to other phosphate metabolites, compared to age-matched controls. In addition, a more alkaline pH is observed in the tumors of treated animals. When the growth delay period ends, nuclear magnetic resonance spectra return to pretreatment patterns. The magnitude of the differences in 31P nuclear magnetic resonance spectral parameters between treated animals and untreated controls is dose dependent. However, doses of cyclophosphamide above 200 mg/kg do not result in earlier spectroscopic alterations, nor in larger effects by Day 3 after treatment, even though clonogenic cell killing and growth delay are greater at these higher doses.

In vivo 31P nuclear magnetic resonance spectroscopy of subcutaneous 9L gliosarcoma: effects of tumor growth and treatment with 1,3-bis(2-chloroethyl)-1-nitrosourea on tumor bioenergetics and histology.

In vivo 31P nuclear magnetic resonance spectroscopy was used to examine the bioenergetics of the rat 9L gliosarcoma during untreated growth and in response to chemotherapy with 1,3-bis(2-chloroethyl)-1-nitrosourea. Tumor growth was associated with a decline in the phosphocreatine and nucleoside triphosphate resonances, consistent with an increase in tumor hypoxia during untreated growth. Following chemotherapy with 1,3-bis(2-chloroethyl)-1-nitrosourea (10 mg/kg), tumor levels of phosphocreatine and nucleoside triphosphate rebounded while the level of inorganic phosphate in the tumor declined. Histological comparison of treated and untreated tumor sections 4 days posttreatment showed that the treated tumor had a lower proportion of necrotic cells, a higher proportion of viable cells, and a 5-fold higher level of interstitial space than the control tumor.

Applications of magnetic resonance spectroscopy to the investigation of neuropsychiatric disorders.

Magnetic resonance spectroscopy (MRS) can noninvasively characterize tissue composition and metabolism in vivo without the need for radioactive isotope administration. For the neuropsychiatrist interested in the functional basis of disease, MRS offers an investigative tool capable of studying a wide variety of neuropsychiatric disorders. This report provides an overview of how MRS works, current and potential clinical applications for specific psychiatric populations, and limitations of the technology.

Effect of ionizing radiation on the human brain: white matter and gray matter T1 in pediatric brain tumor patients treated with conformal radiation therapy.

OBJECTIVE: To test a hypothesis that fractionated radiation therapy (RT) to less than 60 Gy is associated with a dose-related change in the spin-lattice relaxation time (T1) of normal brain tissue, and that such changes are detectable by quantitative MRI (qMRI). METHODS: Each of 21 patients received a qMRI examination before treatment, and at several time points during and after RT. A map of brain T1 was calculated and segmented into white matter and gray matter at each time point. The RT isodose contours were then superimposed upon the T1 map, and changes in brain tissue T1 were analyzed as a function of radiation dose and time following treatment. We used a mixed-model analysis to analyze the longitudinal trend in brain T1 from the start of RT to 1 year later. Predictive factors evaluated included patient age and clinical variables, such as RT dose, time since treatment, and the use of an imaging contrast agent. RESULTS: In white matter (WM), a dose level of greater than 20 Gy was associated with a dose-dependent decrease in T1 over time, which became significant about 3 months following treatment. In gray matter (GM), there was no significant change in T1 over time, as a function of RT doses < 60 Gy. However, GM in close proximity to the tumor had an inherently lower T1 before therapy. Neither use of a contrast agent nor a combination of chemotherapy plus steroids had a significant effect on brain T1. CONCLUSION: Results suggest that T1 mapping may be sensitive to radiation-related changes in human brain tissue T1. WM T1 appears to be unaffected by RT at doses less than approximately 20 Gy; GM T1 does not change at doses less than 60 Gy. However, tumor appears to have an effect upon adjacent GM, even before treatment. Conformal RT may offer a substantial benefit to the patient, by minimizing the volume of normal brain exposed to greater than 20 Gy.

Age-related changes in the pediatric brain: quantitative MR evidence of maturational changes during adolescence.

PURPOSE: To determine whether a quantitative MR imaging method to map spin-lattice relaxation time (T1) can be used to characterize maturational changes in the normal human brain. METHODS: An inversion-recovery technique was used to map T1 transversely at the level of the basal ganglia in a study population of 19 healthy children (4 to 10 years old) and 31 healthy adolescents (10 to 20 years old), and in a normative population of 20 healthy adults (20 to 30 years old). RESULTS: Nonparametric analysis of variance showed that T1 decreases with age in the genu, frontal white matter, caudate, putamen, anterior thalamus, pulvinar nucleus, optic radiation, cortical gray matter (all P < .0001), and occipital white matter. There was a significant reduction in T1 between childhood (mean age, 7.1 +/- 1.4) and adolescence (mean age, 13.5 +/- 2.6) in all brain structures, but there was also a significant reduction in T1 between adolescence (mean age, 13.5 +/- 2.6) and adulthood (mean age, 26.5 +/- 3.4) in all brain structures except occipital white matter. Regression shows that T1 declines to within the range (mean +/- 2 SD) of young adult T1 values by about 2 years in the occipital white matter, by about 4 years in the genu, by 11 years in the cortical gray matter, by 11 years in the frontal white matter, and by 13 years in the thalamus. CONCLUSION: Brain structures mature at strikingly different rates, yet the ratio of gray matter T1 to white matter T1 does not change significantly with age. Thus, conventional MR imaging methods based on inherent contrast are insensitive to these changes. Age-related changes tend to reach completion sooner in white matter than in gray matter tracts. Such normative data are essential for studies of specific pediatric disorders and may be useful for assessing brain maturation in cases of developmental delay.

Prospective evaluation of the brain in asymptomatic children with neurofibromatosis type 1: relationship of macrocephaly to T1 relaxation changes and structural brain abnormalities.

BACKGROUND AND PURPOSE: Mutation of the neurofibromatosis type 1 (NF-1) gene may be associated with abnormal growth control in the brain. Because macrocephaly could be a sign of abnormal brain development and because 30% to 50% of children with NF-1 display macrocephaly in the absence of hydrocephalus, we sought to determine the relationship between macrocephaly and other brain abnormalities in young subjects with NF-1. These subjects were free of brain tumor, epilepsy, or other obvious neurologic problems. METHODS: We prospectively screened 18 neurologically asymptomatic subjects with NF-1, ages 6 to 16 years, using clinical measures, psychometric testing, conventional MR imaging, and quantitative MR imaging to measure T1. RESULTS: Cranial circumference was 2 or more SDs above the age norm in seven (39%) of 18 subjects, a frequency of macrocephaly 17-fold higher than normal. Conventional MR imaging showed abnormalities in all 18 children, although there were more extensive abnormalities in subjects with macrocephaly. Macrocephaly in NF-1 was associated with enlargement of multiple brain structures, and brain T1 in macrocephalic subjects was reduced with respect to controls in the genu, frontal white matter, caudate, putamen, thalamus, and cortex. In normocephalic subjects, T1 was reduced only in the genu and splenium. Volumetric analysis showed that macrocephaly was associated specifically with enlargement of white matter volume. CONCLUSION: Neurologically asymptomatic children with NF-1 showed macrocephaly, cognitive deficit, enlarged brain structures, and abnormally low brain T1. Macrocephaly in children with NF-1 may be associated with characteristic alterations in brain development, marked by more widespread and significant changes in T1, greater enlargement of midline structures, and greater volume of white matter.

More than meets the eye: significant regional heterogeneity in human cortical T1.

Segmented k-space acquisition of data was used to decrease the acquisition time and to increase the imaging resolution of the precise and accurate inversion recovery (PAIR) method of measuring T(1). We validated the new TurboPAIR method by measuring T(1) in 158 regions of interest in 12 volunteers, using both PAIR and TurboPAIR. We found a 3% difference between methods, which could be corrected by linear regression. After validation, the TurboPAIR method was used to test a hypothesis that there is significant regional heterogeneity in cortical T(1). We measured cortical gray matter T(1) in 11 right-handed volunteers, in 48 regions of interest scattered over frontal and parietal cortex, and in 46 ROIs along the central sulcus (CS). We found that T(1) in the CS is less than T(1) elsewhere in the cortex (p<0.001), and that there is considerable hemispheric asymmetry in T(1) in gray matter, but not in white matter. In central gray structures (caudate, thalamus, nucleus pulvinarus), and in the posterior CS (sensory cortex), right hemisphere T(1) was significantly greater than left hemisphere T(1) (p< or =0.004). In cortical gray matter of the frontal lobe and anterior CS (motor cortex), left hemisphere T(1) was significantly greater than right hemisphere T(1) (p< or =0.003). These findings demonstrate that there is considerable regional heterogeneity in human cortical T(1) that is unexplained by differences in tissue iron content, but may be evidence of an inherent anatomic asymmetry of the brain.

Correction of errors caused by imperfect inversion pulses in MR imaging measurement of T1 relaxation times.

Spin-lattice (T1) relaxation times were measured by an inversion-recovery magnetic resonance imaging method with a slice-selective inversion pulse (SIP), a non-selective rectangular inversion pulse (RIP), or a B1-insensitive adiabatic inversion pulse (AIP). Data analysis either assumed perfect inversion (two-parameter fit) or allowed for imperfect inversion (three-parameter fit). Imperfect inversion pulses caused low T1 values in phantoms with a two-parameter fit, while three-parameter T1 estimates were accurate over the range 430-2670 ms. A difference of approximately 10% between two-parameter and three-parameter T1 values in normal human brain tissue was attributed to B1 inhomogeneity with the slice-selective inversion pulse and rectangular inversion pulse, to the slice profile with the slice-selective inversion pulse, and to T2 effects for the adiabatic inversion pulse. Any T1 method that relies on accurate flip angles may have a significant systematic error in vivo. Phantom accuracy does not ensure accuracy in vivo, because phantoms may have a more homogeneous B1 field and a longer T2 than do biological samples.

Effect of a gadodiamide contrast agent on the reliability of brain tissue T1 measurements.

To determine whether brain spin-lattice relaxation time (T1) can routinely be measured after contrast-agent injection, we measured T1 by a precise and accurate inversion-recovery (PAIR) method in five brain tumor patients, before and again after contrast-agent injection. The T1 in at least 20 regions of interest (ROIs) was measured in each patient, avoiding areas of contrast enhancement visible by conventional MR imaging. Contrast-agent injection reduced T1 in 51 regions of interest in white matter by less than 1% (not significant), and in 50 regions of interest in gray matter by less than 2% (p = 0.001). Pixel-by-pixel plots demonstrate that T1 is reduced substantially in extra-parenchymal tissues, but not in brain tissues. Therefore, T1 mapping with the precise and accurate inversion-recovery method can routinely be done after contrast injection. Our results suggest that the precise and accurate inversion-recovery method is not sensitive to the T1 of blood in the presence of an intact blood-brain barrier, although a substantial T1 reduction does occur in the absence of a blood-brain barrier.

Hybrid artificial neural network segmentation of precise and accurate inversion recovery (PAIR) images from normal human brain.

This paper presents a novel semi-automated segmentation and classification method based on raw signal intensities from a quantitative T1 relaxation technique with two novel approaches for the removal of partial volume effects. The segmentation used a Kohonen Self Organizing Map that eliminated inter- and intra-operator variability. A Multi-layered Backpropagation Neural Network was able to classify the test data with a predicted accuracy of 87.2% when compared to manual classification. A linear interpolation of the quantitative T1 information by region and on a pixel-by-pixel basis was used to redistribute voxels containing a partial volume of gray matter (GM) and white matter (WM) or a partial volume of GM and cerebrospinal fluid (CSF) into the principal components of GM, WM, and CSF. The method presented was validated against manual segmentation of the base images by three experienced observers. Comparing segmented outputs directly to the manual segmentation revealed a difference of less than 2% in GM and less than 6% in WM for pure tissue estimations for both the regional and pixel-by-pixel redistribution techniques. This technique produced accurate estimates of the amounts of GM and WM while providing a reliable means of redistributing partial volume effects.