Biomedical subjects

Trevor Hastie

Publications and source records attributed to Trevor Hastie.

At least 19 recordsLinked to original sources

PubMed2006

Regularized linear discriminant analysis and its application in microarrays.

In this paper, we introduce a modified version of linear discriminant analysis, called the "shrunken centroids regularized discriminant analysis" (SCRDA). This method generalizes the idea of the "nearest shrunken centroids" (NSC) (Tibshirani and others, 2003) into the classical discriminant analysis. The SCRDA method is specially designed for classification problems in high dimension low sample size situations, for example, microarray data. Through both simulated data and real life data, it is shown that this method performs very well in multivariate classification problems, often outperforms the PAM method (using the NSC algorithm) and can be as competitive as the support vector machines classifiers. It is also suitable for feature elimination purpose and can be used as gene selection method. The open source R package for this method (named "rda") is available on CRAN (http://www.r-project.org) for download and testing.

Computer Simulation↗

PubMed2006

Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers.

BACKGROUND: Inadequate oxygen (hypoxia) triggers a multifaceted cellular response that has important roles in normal physiology and in many human diseases. A transcription factor, hypoxia-inducible factor (HIF), plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1alpha protein. Despite the ubiquity and importance of hypoxia responses, little is known about the variation in the global transcriptional response to hypoxia among different cell types or how this variation might relate to tissue- and cell-specific diseases. METHODS AND FINDINGS: We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells, breast epithelial cells, smooth muscle cells, and endothelial cells with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This heightened response was associated with a uniquely high level of HIF-1alpha RNA in renal cells, and it could be diminished by reducing HIF-1alpha expression via RNA interference. A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in breast and ovarian cancers. In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use. CONCLUSIONS: The transcriptional response to hypoxia varies among human cells. Some of this variation is traceable to variation in expression of the HIF1A gene. A gene-expression signature of the cellular response to hypoxia is associated with a significantly poorer prognosis in breast and ovarian cancer.

Adult↗

PubMed2005

Microarray analysis of the transcriptional response to single or multiple doses of ionizing radiation in human subcutaneous fibroblasts.

BACKGROUND AND PURPOSE: Transcriptional profiling of fibroblasts derived from breast cancer patients might improve our understanding of subcutaneous radiation-induced fibrosis. The aim of this study was to get a comprehensive overview of the changes in gene expression in subcutaneous fibroblast cell lines after various ionizing radiation (IR) schemes in order to provide information on potential targets for prevention and to suggest candidate genes for SNP association studies aimed at predicting individual risk of radiation-induced morbidity. PATIENTS AND METHODS: Thirty different human fibroblast cell lines were included in the study, and two different radiation schemes; single dose experiments with 3.5 Gy or fractionated with 3 x 3.5 Gy. Expression analyses were performed on unexposed and exposed cells after different time points. The IR response was analyzed using the statistical method Significance Analysis of Microarrays (SAM). RESULTS: While many of the identified genes were involved in known IR response pathways like cell cycle arrest, proliferation and detoxification, a substantial fraction of the genes were involved in processes not previously associated with IR response. Of particular interest is genes involved in ECM remodelling, Wnt signalling and IGF signalling. Many of the genes were identified after a single dose, but transcriptional changes in genes related to ROS scavenging and ECM remodelling were most profound after a fractionated scheme. CONCLUSIONS: We have identified a number of IR response pathways in fibroblasts derived from breast cancer patients. Besides previously identified pathways, we have identified new pathways and genes that could be relevant for prevention and intervention studies of subcutaneous radiation-induced fibrosis as well as being candidates for SNP association studies.

Breast Neoplasms↗

PubMed2005

Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival.

Based on the hypothesis that features of the molecular program of normal wound healing might play an important role in cancer metastasis, we previously identified consistent features in the transcriptional response of normal fibroblasts to serum, and used this "wound-response signature" to reveal links between wound healing and cancer progression in a variety of common epithelial tumors. Here, in a consecutive series of 295 early breast cancer patients, we show that both overall survival and distant metastasis-free survival are markedly diminished in patients whose tumors expressed this wound-response signature compared to tumors that did not express this signature. A gene expression centroid of the wound-response signature provides a basis for prospectively assigning a prognostic score that can be scaled to suit different clinical purposes. The wound-response signature improves risk stratification independently of known clinico-pathologic risk factors and previously established prognostic signatures based on unsupervised hierarchical clustering ("molecular subtypes") or supervised predictors of metastasis ("70-gene prognosis signature").

Breast Neoplasms↗

PubMed2005

Quantitative measurements of alternating finger tapping in Parkinson's disease correlate with UPDRS motor disability and reveal the improvement in fine motor control from medication and deep brain stimulation.

The Unified Parkinson's Disease Rating Scale (UPDRS) is the primary outcome measure in most clinical trials of Parkinson's disease (PD) therapeutics. Each subscore of the motor section (UPDRS III) compresses a wide range of motor performance into a coarse-grained scale from 0 to 4; the assessment of performance can also be subjective. Quantitative digitography (QDG) is an objective, quantitative assessment of digital motor control using a computer-interfaced musical keyboard. In this study, we show that the kinematics of a repetitive alternating finger-tapping (RAFT) task using QDG correlate with the UPDRS motor score, particularly with the bradykinesia subscore, in 33 patients with PD. We show that dopaminergic medication and an average of 9.5 months of bilateral subthalamic nucleus deep brain stimulation (B-STN DBS) significantly improve UPDRS and QDG scores but may have different effects on certain kinematic parameters. This study substantiates the use of QDG to measure motor outcome in trials of PD therapeutics and shows that medication and B-STN DBS both improve fine motor control.

Biomechanical Phenomena↗

PubMed2005

Patient-derived health state utilities for gastroesophageal reflux disease.

BACKGROUND AND AIMS: Gastroesophageal reflux disease is a chronic disease that adversely affects health-related quality of life. The purpose of this study was to derive health state utilities for patients with chronic heartburn symptoms. METHODS: We used a custom-designed computer program in order to elicit utilities with the time-tradeoff and standard-gamble techniques. Patients with chronic (more than 6 months) symptoms of gastroesophageal reflux disease entered the study. Two interviews were performed in random sequence either initially on medications for heartburn that adequately controlled symptoms, or off of medications for 1 wk while the patient was symptomatic. We also collected data using visual-analog scales, quality of life in reflux and dyspepsia (QOLRAD), and Gastrointestinal Symptom Rating Scale (GSRS) scores. RESULTS: We invited 222 patients to participate; 158 (71%) patients (129 men, 29 women) completed the study. Barrett's esophagus was present in 40 (25%), erosive disease in 17 (11%), and 118 (74%) had comorbid conditions. The mean (+/-SD) utility ratings were 0.94 +/- 0.09 on medical therapy and 0.90 +/- 0.12 off medications for patients with reflux alone using time tradeoff (p= 0.004), and 0.94 +/- 8.0 both on and off of antireflux medications with standard-gamble assessment (p= 0.96). Mean time-tradeoff scores were also significantly lower off of medications for patients with other comorbid conditions (p= 0.002). There was no significant difference between mean utility scores for patients with or without Barrett's esophagus or erosive disease. CONCLUSION: Gastroesophageal reflux disease adversely affects health-related quality of life. Time-tradeoff utility for patients with reflux disease is substantially higher when patients are on medication than off medications.

Adult↗

PubMed2004

Sample classification from protein mass spectrometry, by 'peak probability contrasts'.

MOTIVATION: Early cancer detection has always been a major research focus in solid tumor oncology. Early tumor detection can theoretically result in lower stage tumors, more treatable diseases and ultimately higher cure rates with less treatment-related morbidities. Protein mass spectrometry is a potentially powerful tool for early cancer detection. We propose a novel method for sample classification from protein mass spectrometry data. When applied to spectra from both diseased and healthy patients, the 'peak probability contrast' technique provides a list of all common peaks among the spectra, their statistical significance and their relative importance in discriminating between the two groups. We illustrate the method on matrix-assisted laser desorption and ionization mass spectrometry data from a study of ovarian cancers. RESULTS: Compared to other statistical approaches for class prediction, the peak probability contrast method performs as well or better than several methods that require the full spectra, rather than just labelled peaks. It is also much more interpretable biologically. The peak probability contrast method is a potentially useful tool for sample classification from protein mass spectrometry data.

Algorithms↗

PubMed2004

Efficient quadratic regularization for expression arrays.

Gene expression arrays typically have 50 to 100 samples and 1000 to 20,000 variables (genes). There have been many attempts to adapt statistical models for regression and classification to these data, and in many cases these attempts have challenged the computational resources. In this article we expose a class of techniques based on quadratic regularization of linear models, including regularized (ridge) regression, logistic and multinomial regression, linear and mixture discriminant analysis, the Cox model and neural networks. For all of these models, we show that dramatic computational savings are possible over naive implementations, using standard transformations in numerical linear algebra.

Data Interpretation, Statistical↗

PubMed2004

Classification of gene microarrays by penalized logistic regression.

Classification of patient samples is an important aspect of cancer diagnosis and treatment. The support vector machine (SVM) has been successfully applied to microarray cancer diagnosis problems. However, one weakness of the SVM is that given a tumor sample, it only predicts a cancer class label but does not provide any estimate of the underlying probability. We propose penalized logistic regression (PLR) as an alternative to the SVM for the microarray cancer diagnosis problem. We show that when using the same set of genes, PLR and the SVM perform similarly in cancer classification, but PLR has the advantage of additionally providing an estimate of the underlying probability. Often a primary goal in microarray cancer diagnosis is to identify the genes responsible for the classification, rather than class prediction. We consider two gene selection methods in this paper, univariate ranking (UR) and recursive feature elimination (RFE). Empirical results indicate that PLR combined with RFE tends to select fewer genes than other methods and also performs well in both cross-validation and test samples. A fast algorithm for solving PLR is also described.

Algorithms↗

PubMed2004

Microelectrode recording revealing a somatotopic body map in the subthalamic nucleus in humans with Parkinson disease.

OBJECT: The subthalamic nucleus (STN) is a key structure for motor control through the basal ganglia. The aim of this study was to show that the STN in patients with Parkinson disease (PD) has a somatotopic organization similar to that in nonhuman primates. METHODS: A functional map of the STN was obtained using electrophysiological microrecording during placement of deep brain stimulation (DBS) electrodes in patients with PD. Magnetic resonance imaging was combined with ventriculography and intraoperative x-ray film to assess the position of the electrodes and the STN units, which were activated by limb movements to map the sensorimotor region of the STN. Each activated cell was located relative to the anterior commissure-posterior commissure line. Three-dimensional coordinates of the cells were analyzed statistically to determine whether those cells activated by movements of the arm and leg were segregated spatially. Three hundred seventy-nine microelectrode tracks were created during placement of 71 DBS electrodes in 44 consecutive patients. Somatosensory driving was found in 288 tracks. The authors identified and localized 1213 movement-related cells and recorded responses from 29 orofacial cells, 480 arm-related cells, 558 leg-related cells, and 146 cells responsive to both arm and leg movements. Leg-related cells were localized in medial (p < 0.0001) and ventral (p < 0.0004) positions and tended to be situated anteriorly (p = 0.063) relative to arm-related cells. CONCLUSIONS: Evidence of somatotopic organization in the STN in patients with PD supports the current theory of highly segregated loops integrating cortex-basal ganglia connections. These loops are preserved in chronic degenerative diseases such as PD, but may subserve a distorted body map. This finding also supports the relevance of microelectrode mapping in the optimal placement of DBS electrodes along the subthalamic homunculus.

Brain Mapping↗

PubMed2004

Mitral annular size predicts Alfieri stitch tension in mitral edge-to-edge repair.

BACKGROUND AND AIM OF THE STUDY: Whilst increased 'Alfieri stitch' tension may reduce the durability of 'edge-to-edge' mitral repair, the factors affecting suture tension are unknown. In order to study hemodynamics and left ventricular (LV) and annular dynamics that determine suture tension, the central edge of the mitral leaflets was approximated with a miniature force transducer to measure leaflet tension (T) at the leaflet approximation point. METHODS: Eight sheep were studied under open-chest conditions immediately after surgical placement of a force transducer and implantation of radiopaque markers on the left ventricle and mitral annulus (MA). Hemodynamic variables were altered by two caval occlusion steps (deltaV1 and deltaV2) and dobutamine infusion. Three-dimensional marker coordinates were obtained by simultaneous biplane videofluoroscopy to measure LV volume, MA area (MAA) and septal-lateral (SL) annular dimension throughout the cardiac cycle. RESULTS: At baseline, peak Alfieri stitch tension (0.30 +/- 0.18 N) was observed 96 +/- 61 ms prior to end-diastole coincident with peak annular SL diameter (98 +/- 58 ms before end-diastole). Dobutamine infusion decreased suture tension (from 0.30 +/- 0.18 N to 0.20 +/- 0.12 N, p = 0.01), although peak systolic pressure increased significantly (138 +/- 19 versus 115 +/- 14 mmHg; p = 0.03). A regression model was fitted with the goal of interpreting the hemodynamic and geometric predictors of tension as their influence varied with time: Tt (N) = 0.1916 + 0.2115 x SL (cm) - 0.1996 x MAA/SL (cm2/cm) + ft x LVP (mmHg), where Tt is tension at any time during the cardiac cycle and ft is the time-varying coefficient of LVP. CONCLUSION: Tension on the leaflets in the edge-to-edge repair is determined primarily by MA SL size, and paradoxically is lower when the contractile state is enhanced. This indicates that annular and/or LV dilatation increase stitch tension and may adversely affect durability of the repair if concomitant ring annuloplasty is not performed.

Animals↗

PubMed2003

Gene expression patterns in ovarian carcinomas.

We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.

Adenocarcinoma↗

PubMed2003

Repeated observation of breast tumor subtypes in independent gene expression data sets.

Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into one basal-like, one ERBB2-overexpressing, two luminal-like, and one normal breast tissue-like subgroup. The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment. Similar cluster analyses of two published, independent data sets representing different patient cohorts from different laboratories, uncovered some of the same breast cancer subtypes. In the one data set that included information on time to development of distant metastasis, subtypes were associated with significant differences in this clinical feature. By including a group of tumors from BRCA1 carriers in the analysis, we found that this genotype predisposes to the basal tumor subtype. Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities.

Breast Neoplasms↗

PubMed2003

Post-transplantation lymphoproliferative disease in heart and heart-lung transplant recipients: 30-year experience at Stanford University.

BACKGROUND: Post-transplantation lymphoproliferative disease (PTLD) is an important source of morbidity and mortality in transplant recipients, with a reported incidence of 0.8% to 20%. Risk factors are thought to include immunosuppressive agents and viral infection. This study attempts to evaluate the impact of different immunosuppressive regimens, ganciclovir prophylaxis and other potential risk factors in the development of PTLD. METHODS: We reviewed the records of 1026 (874 heart, 152 heart-lung) patients who underwent transplantation at Stanford between 1968 and 1997. Of these, 57 heart and 8 heart-lung recipients developed PTLD. During this interval, 4 different immunosuppressive regimens were utilized sequentially. In January 1987, ganciclovir prophylaxis for cytomegalovirus serologic-positive patients was introduced. Other potential risk factors evaluated included age, gender, prior cardiac diagnoses, HLA match, rejection frequency and calcium-channel blockade. RESULTS: No correlation of development of PTLD was found with different immunosuppression regimens consisting of azathioprine, prednisone, cyclosporine, OKT3 induction, tacrolimus and mycophenolate mofetil. A trend suggesting an influence of ganciclovir on the prevention of PTLD was not statistically significant (p = 0.12). Recipient age and rejection frequency, as well as high-dose cyclosporine immunosuppression, were significantly (p < 0.02) associated with PTLD development. The prevalence of PTLD at 13.3 years was 15%. CONCLUSIONS: The overall incidence of PTLD was 6.3%. It was not altered by sequential modifications in treatment regimens. Younger recipient age and higher rejection frequency were associated with increased PTLD occurrence. The 15% prevalence of PTLD in 58 long-term survivors was unexpectedly high.

Adolescent↗

PubMed2003

Ischemia in three left ventricular regions: Insights into the pathogenesis of acute ischemic mitral regurgitation.

BACKGROUND: Acute posterolateral left ventricular ischemia in sheep results in ischemic mitral regurgitation, but the effects of ischemia in other left ventricular regions on ischemic mitral regurgitation is unknown. METHODS: Six adult sheep had radiopaque markers placed on the left ventricle, mitral annulus, and anterior and posterior mitral leaflets at the valve center and near the anterior and posterior commissures. After 6 to 8 days, animals were studied with biplane videofluoroscopy and transesophageal echocardiography before and during sequential balloon occlusion of the left anterior descending, distal left circumflex, and proximal left circumflex coronary arteries. Time of valve closure was defined as the time when the distance between leaflet edge markers reached its minimum plateau, and systolic leaflet edge separation distance was calculated on the basis of left ventricular ejection. RESULTS: Only proximal left circumflex coronary artery occlusion resulted in ischemic mitral regurgitation, which was central and holosystolic. Delayed valve closure (anterior commissure, 58 +/- 29 vs 92 +/- 24 ms; valve center, 52 +/- 26 vs 92 +/- 23 ms; posterior commissure, 60 +/- 30 vs 94 +/- 14 ms; all P <.05) and increased leaflet edge separation distance during ejection (mean increase, 2.2 +/- 1.5 mm, 2.1 +/- 1.9 mm, and 2.1 +/- 1.5 mm at the anterior commissure, valve center, and posterior commissure, respectively; P <.05 for all) was seen during proximal left circumflex coronary artery occlusion but not during left anterior descending or distal left circumflex coronary artery occlusion. Ischemic mitral regurgitation was associated with a 19% +/- 10% increase in mitral annular area, and displacement of both papillary muscle tips away from the septal annulus at end systole. CONCLUSIONS: Acute ischemic mitral regurgitation in sheep occurred only after proximal left circumflex coronary artery occlusion along with delayed valve closure in early systole and increased leaflet edge separation throughout ejection in all 3 leaflet coaptation sites. The degree of left ventricular systolic dysfunction induced did not correlate with ischemic mitral regurgitation, but both altered valvular and subvalvular 3-dimensional geometry were necessary to produce ischemic mitral regurgitation during acute left ventricular ischemia.

Acute Disease↗

PubMed2003

Note on "Comparison of model selection for regression" by Vladimir Cherkassky and Yunqian Ma.

While Cherkassky and Ma (2003) raise some interesting issues in comparing techniques for model selection, their article appears to be written largely in protest of comparisons made in our book, Elements of Statistical Learning (2001). Cherkassky and Ma feel that we falsely represented the structural risk minimization (SRM) method, which they defend strongly here. In a two-page section of our book (pp. 212-213), we made an honest attempt to compare the SRM method with two related techniques, Aikaike information criterion (AIC) and Bayesian information criterion (BIC). Apparently, we did not apply SRM in the optimal way. We are also accused of using contrived examples, designed to make SRM look bad. Alas, we did introduce some careless errors in our original simulation--errors that were corrected in the second and subsequent printings. Some of these errors were pointed out to us by Cherkassky and Ma (we supplied them with our source code), and as a result we replaced the assessment "SRM performs poorly overall" with a more moderate "the performance of SRM is mixed" (p. 212).

Models, Neurological↗

PubMed2002

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.

BACKGROUND: T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3-3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. CONCLUSION: T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.

Journal Article↗

PubMed2002

Diagnosis of multiple cancer types by shrunken centroids of gene expression.

We have devised an approach to cancer class prediction from gene expression profiling, based on an enhancement of the simple nearest prototype (centroid) classifier. We shrink the prototypes and hence obtain a classifier that is often more accurate than competing methods. Our method of "nearest shrunken centroids" identifies subsets of genes that best characterize each class. The technique is general and can be used in many other classification problems. To demonstrate its effectiveness, we show that the method was highly efficient in finding genes for classifying small round blue cell tumors and leukemias.

Child↗