Jerry Halpern

Prognostic significance of actual dose intensity in diffuse large-cell lymphoma: results of a tree-structured survival analysis.

While diffuse large-cell lymphoma (DLCL) is considered to be highly curable with current therapy, treatment failures are observed even with intensive combination chemotherapy regimens. In order to study the prognostic significance of actual dose intensity of chemotherapy in DLCL, we retrospectively analyzed 115 previously untreated patients treated as Stanford between 1975 and 1986 with cyclophosphamide, Adriamycin (doxorubicin; Adria Laboratories, Columbus, OH), vincristine, and prednisone (CHOP), methotrexate, bleomycin, Adriamycin, cyclophosphamide, vincristine, and dexamethasone ([M]BACOD), or methotrexate, Adriamycin, cyclosphosphamide, vincristine, prednisone, and bleomycin (MACOP-B). The actual relative dose intensity (RDI), the amount of drug actually administered to each patient during the first 12 weeks of therapy, was calculated as standardized to CHOP and analyzed in addition to clinical factors prognostic for survival by univariate analysis. Multivariate recursive partitioning (tree-structured) survival analysis identified the actual RDI of Adriamycin greater than 75% as the single most important predictor of survival. A model incorporating the actual RDI of Adriamycin and performance status, in combination with serum lactate dehydrogenase (LDH) and extranodal disease, defined three overall prognostic groups of patients with respective 3-year survival rates of 89%, 63%, and 18%. The three prognostic groups remained distinct, even when restricted to complete responders. This model was also predictive of survival when dose intensity was analyzed relative to the optimum dose defined for each of the three regimens and when applied to a subgroup of patients aged 50 years or younger. We conclude that actual RDI is an important prognostic factor for survival in DLCL and that analysis of RDI early in the course of treatment may allow modification of the treatment plan.

A class of tests for linkage using affected pedigree members

We describe a class of nonparametric tests for linkage between a marker and a gene assumed to exist and to govern susceptibility to a disease. The tests are formed by assigning a score to each possible pattern of marker allele sharing (identity-by-descent) among affected pedigree members, and then averaging the scores over all patterns compatible with the observed marker genotype and genealogical relationship of the affected members. Different score functions give different tests. One function, which examines marker allele similarity across pairs of affected pedigree members, gives a test similar to that of Fimmers et al. (1989, in Multipoint Mapping and Linkage Based on Affected Pedigree Members: Genetic Analysis Workshop, R. C. Elston, M. A. Spence, S. E. Hodge, and J. W. MacCluer (eds), 123-128; City: Alan R. Liss). A second function examines allele similarity across arbitrary subsets, not just pairs, of affected members. The resulting test can be more powerful than the one based solely on pairs of affected members. The approach has several advantages: it does not require knowledge of the mode of disease inheritance; it does not require unambiguous determination of identity-by-descent at the marker; it does not suffer from variability due to chance allele similarity among affected members who are unrelated, such as spouses; it allows marker genotypes of unaffected members to contribute information on allele sharing among the affected; it permits calculation of exact P-values. Computational requirements limit the tests to many pedigrees with few (< 16) affected members.

Long-term survival after histologic transformation of low-grade follicular lymphoma.

PURPOSE To describe the course of patients following histologic transformation (HT) from low-grade follicular lymphoma to intermediate- or high-grade non-Hodgkins lymphoma. PATIENTS AND METHODS Patients were identified from data bases in the Division of Oncology and the Department of Surgical Pathology. HT was defined as the conversion of a follicular small cleaved-cell or follicular mixed small cleaved-cell and large-cell lymphoma to a diffuse large-cell, diffuse mixed small cleaved-cell and large-cell or any high-grade lymphoma. RESULTS We analyzed the clinical course of 74 low-grade lymphoma patients with histologically proven transformation occurring from 1965 to 1988. The median time from diagnosis to HT was 66 months, and the median age at HT was 58 years. The median duration of survival after transformation was 22 months. Anatomic extent of disease at HT (limited v extensive, P = .01), prior chemotherapy (none v any, P = .01), and response to therapy (complete v partial or none, P = .005) at time of HT were identified as significant predictors of survival after HT in backward-selection Cox regression analysis. Thirty patients attained a complete response to therapy at HT. They had a median survival duration of 81 months after HT. CONCLUSION A subset of patients with HT from low-grade follicular lymphoma to intermediate- or high-grade lymphoma enjoys relatively long-term survival. Patients with limited disease and no previous exposure to chemotherapy have the most favorable prognosis.

Maximally Selected Chi Square Statistics for Small Samples

Two samples can be compared by selecting a cut point and forming a 2 x 2 table of the numbers of observations above and below the cut point in each sample. Different cut points correspond to the maximum chi square statistic, the maximum squared log odds ratio, and the generalized Kolmogorov-Smirnov statistic. We simulated the small-sample null distribution of these statistics. The distributions of the maximally selected chi square statistic and the squared log odds ratio statistic are compared to each other and to the large-sample results of Miller and Siegmund (1982, Biometrics 38, 1011-1016. The distributions of and agreement among the three cut points are also considered.

Early precursors of pancreatic cancer in college men

From college data on 50,000 male former students, the records of 126 men who died of pancreatic cancer in a 16-50 yr follow-up period were compared with those of 504 surviving classmates with respect to physical and social characteristics. Return mail questionnaires received from 30,000 surviving alumni in 1962 or 1966 also were reviewed for characteristics that might predict altered risk of pancreatic cancer. Strong positive associations were found for cigarette smoking as reported both during college (p less than 0.001) and at time of questionnaire return (p = 0.03). Smoking 10 or more cigarettes per day during college corresponded to a relative risk of 2.6 with 95% confidence limits 1.5 to 4.6, and a positive smoking history at questionnaire return yielded a relative risk of 2.4 (1.1-5.1). No association was found for collegiate coffee drinking, either before or after adjustment for cigarette smoking. The relative risk for coffee drinking adjusted for smoking was 1.1 (0.7-1.8). In contrast, collegiate tea consumption was associated with a reduction in pancreatic cancer risk. The relative risk for tea drinking adjusted for smoking was 0.5 (0.3-0.9). Men who at college physical examination complained of occasional abdominal pain or discomfort had increased relative risk of pancreatic cancer (3.1 : 1.1-9.0) in the follow-up period.

A Genome Screen of Families with Multiple Cases of Prostate Cancer: Evidence of Genetic Heterogeneity

We conducted a genomewide screen for prostate cancer-susceptibility genes on the basis of data from 98 families from the United States and Canada that had three or more verified diagnoses of prostate cancer among first- and second-degree relatives. We found a statistically significant excess of markers for which affected relatives exhibited modest amounts of excess allele-sharing; however, no single chromosomal region contained markers with excess allele-sharing of sufficient magnitude to indicate unequivocal evidence of linkage. Positive linkage signals of nominal statistical significance were found in two regions (5p-q and 12p) that have been identified as weakly positive in other data sets and in region 19p, which has not been identified previously. All these signals were considerably stronger for analyses restricted to families with mean age at onset below the median than for analyses of families with mean age at onset above the median. The data provided little support for any of the putative prostate cancer-susceptibility genes identified in other linkage studies.

MULTI‐STAGE SAMPLING IN GENETIC EPIDEMIOLOGY

When data are expensive to collect, it can be cost-efficient to sample in two or more stages. In the first stage a simple random sample is drawn and then stratified according to some easily measured attribute. In each subsequent stage a random subset of previously selected units is sampled for more detailed observation, with a units sampling probability determined by its attributes as observed in the previous stages. These designs are useful in many medical studies; here we use them in genetic epidemiology. Two genetic studies illustrate the strengths and limitations of the approach. The first study evaluates nuclear and mitochondrial DNA in U.S. blacks. The goal is to estimate the relative contributions of white male genes and white female genes to the gene pool of African-Americans. This example shows that the Horvitz-Thompson estimators proposed for multi-stage designs can be inefficient, particularly when used with unnecessary stratification. The second example is a multi-stage study of familial prostate cancer. The goal is to gather pedigrees, blood samples and archived tissue for segregation and linkage analysis of familial prostate cancer data by first obtaining crude family data from prostate cancer cases and cancer-free controls. This second example shows the gains in efficiency from multi-stage sampling when the individual likelihood or quasilikelihood scores vary substantially across strata.

Multipoint Linkage Analysis

Multipoint linkage analysis is commonly used to evaluate linkage of a disease to multiple markers in a small region. Multipoint analysis is particularly powerful when the IBD relations of family members at the trait locus are ambiguous. The increased power arises because, unlike single-marker analyses, multipoint analysis uses haplotype information from several markers to infer the IBD relations. We wish to temper this advantage with a cautionary note: multipoint analysis is sensitive to power loss due to misspecification of intermarker distances. Such misspecification is especially problematic when dealing with closely spaced markers. We present computer simulations comparing the power of single-point and multipoint analyses, both when IBD relations are ambiguous, and when the intermarker distances are misspecified. We conclude that when evaluating markers in a small region to confirm or refute previous findings, a situation in which p values of modest statistical significance are important, single marker analyses may provide more reliable measures of the strength of support for linkage than multipoint statistics.

Designing clinical trials with arbitrary specification of survival functions and for the log rank or generalized Wilcoxon test

This article describes a computer program that allows interactive determination of the length of accrual period and follow-up period sufficient to assure desired level of significance and power. The program allows for arbitrary specification of the hypothesized survival curves and the alternative survival curve. It allows use of either the generalized Wilcoxon test or the log rank test. The program can be run on an IBM personal computer.

Probability of gene identity by descent : computation and applications

Two genes at a given locus are identical by descent (IBD) if both have been inherited from a common ancestor. We present an algorithm for computing the probabilities of all IBD relationships among the genes of pedigree members. We show how to use these probabilities to calculate the probability of any combination of genotypes or phenotypes for the pedigree members. Applications to linkage analysis and genetic counseling are illustrated with examples. The algorithm also can be used to calculate the generalized kinship coefficients proposed by others.