RESUMEN
Genome-wide association mapping and genomic predictions of phenotype of individuals in livestock are predominately based on the detection and estimation of additive genetic effects. Non-additive genetic effects are largely ignored. Studies in animals, plants, and humans to assess the impact of non-additive genetic effects in genetic analyses have led to differing conclusions. In this paper, we examined the consequences of including non-additive genetic effects in genome-wide association mapping and genomic prediction of total genetic values in a commercial population of 5,658 broiler chickens genotyped for 45,176 single nucleotide polymorphism (SNP) markers. We employed mixed-model equations and restricted maximum likelihood to analyze 7 feed related traits (TRT1 - TRT7). Dominance variance accounted for a significant proportion of the total genetic variance in all 7 traits, ranging from 29.5% for TRT1 to 58.4% for TRT7. Using a 5-fold cross-validation schema, we found that in spite of the large dominance component, including the estimated dominance effects in the prediction of total genetic values did not improve the accuracy of the predictions for any of the phenotypes. We offer some possible explanations for this counter-intuitive result including the possible confounding of dominance deviations with common environmental effects such as hatch, different directional effects of SNP additive and dominance variations, and the gene-gene interactions' failure to contribute to the level of variance.
Asunto(s)
Pollos/genética , Variación Genética , Estudio de Asociación del Genoma Completo , Animales , Pollos/fisiología , Dieta/veterinaria , Conducta Alimentaria , Femenino , Masculino , Modelos Genéticos , FenotipoRESUMEN
We introduce an innovative approach to lowering the overall cost of obtaining genomic EBV (GEBV) and encourage their use in commercial extensive herds of Brahman beef cattle. In our approach, the DNA genotyping of cow herds from 2 independent properties was performed using a high-density bovine SNP chip on DNA from pooled blood samples, grouped according to the result of a pregnancy test following their first and second joining opportunities. For the DNA pooling strategy, 15 to 28 blood samples from the same phenotype and contemporary group were allocated to pools. Across the 2 properties, a total of 183 pools were created representing 4,164 cows. In addition, blood samples from 309 bulls from the same properties were also taken. After genotyping and quality control, 74,584 remaining SNP were used for analyses. Pools and individual DNA samples were related by means of a "hybrid" genomic relationship matrix. The pooled genotyping analysis of 2 large and independent commercial populations of tropical beef cattle was able to recover significant and plausible associations between SNP and pregnancy test outcome. We discuss 24 SNP with significant association ( < 1.0 × 10) and mapped within 40 kb of an annotated gene. We have established a method to estimate the GEBV in young herd bulls for a trait that is currently unable to be predicted at all. In summary, our novel approach allowed us to conduct genomic analyses of fertility in 2 large commercial Brahman herds managed under extensive pastoral conditions.
Asunto(s)
Bovinos/genética , Bovinos/fisiología , Fertilidad , Animales , Cruzamiento , Bovinos/clasificación , Femenino , Estudio de Asociación del Genoma Completo , Masculino , Linaje , Polimorfismo de Nucleótido Simple , Embarazo , Carne RojaRESUMEN
Pooled genomic DNA has been proposed as a cost-effective approach in genomewide association studies (GWAS). However, algorithms for genotype calling of biallelic SNP are not adequate with pooled DNA samples because they assume the presence of 2 fluorescent signals, 1 for each allele, and operate under the expectation that at most 2 copies of the variant allele can be found for any given SNP and DNA sample. We adapt analytical methodology from 2-channel gene expression microarray technology to SNP genotyping of pooled DNA samples. Using 5 datasets from beef cattle and broiler chicken of varying degrees of complexity in terms of design and phenotype, continuous and dichotomous, we show that both differential hybridization (M = green minus red intensity signal) and abundance (A = average of red and green intensities) provide useful information in the prediction of SNP allele frequencies. This is predominantly true when making inference about extreme SNP that are either nearly fixed or highly polymorphic. We propose the use of model-based clustering via mixtures of bivariate normal distributions as an optimal framework to capture the relationship between hybridization intensity and allele frequency from pooled DNA samples. The range of M and A values observed here are in agreement with those reported within the context of gene expression microarray and also with those from SNP array data within the context of analytical methodology for the identification of copy number variants. In particular, we confirm that highly polymorphic SNP yield a strong signal from both channels (red and green) while lowly or nonpolymorphic SNP yield a strong signal from 1 channel only. We further confirm that when the SNP allele frequencies are known, either because the individuals in the pools or from a closely related population are themselves genotyped, a multiple regression model with linear and quadratic components can be developed with high prediction accuracy. We conclude that when these approaches are applied to the estimation of allele frequencies, the resulting estimates allow for the development of cost-effective and reliable GWAS.
Asunto(s)
Bovinos/genética , Pollos/genética , ADN/genética , Genotipo , Animales , Biometría , Femenino , Masculino , Polimorfismo de Nucleótido SimpleRESUMEN
Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.
Asunto(s)
Acuicultura/métodos , Cruzamiento/métodos , Marcadores Genéticos/genética , Salmo salar/genética , Procesos de Determinación del Sexo/genética , Animales , Mapeo Cromosómico , Cartilla de ADN/genética , Femenino , Genotipo , Masculino , Repeticiones de Microsatélite/genética , Reacción en Cadena de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa/veterinaria , TasmaniaRESUMEN
The aim of this study was to fine map the genomic location of the Horns locus in the Australian Merino sheep population and to identify markers that can be used to predict the horn phenotype. A linkage disequilibrium analysis of horn data from Australian Merino sheep mapped the Horns locus to a small region on chromosome 10. A single nucleotide polymorphism in the region was found to be highly predictive for the polled phenotype in an experimental population of Merino sheep. This was owing to a dominance effect of one of the alleles when inherited maternally. It was suggested that a genetic test would provide a good predictor of the polled phenotype. Finally, an evaluation of industry data showed that the SNP is at very different frequencies in Poll Merino sheep that have been bred for polledness (based on phenotype alone) compared with the Merino sheep breed.
Asunto(s)
Cromosomas de los Mamíferos/genética , Cuernos , Fenotipo , Polimorfismo de Nucleótido Simple , Ovinos/genética , Alelos , Animales , Australia , Cruzamiento , Mapeo Cromosómico , Femenino , Sitios Genéticos , Genoma , Desequilibrio de Ligamiento , MasculinoRESUMEN
The objective of the study was to test the effectiveness of a new type of conductivity sensor, along with vaginal temperature, at identifying the LH peak associated with estrus in dairy cows. Twelve mature non-lactating Holstein-Friesian cows had their estrous cycles synchronized on two occasions, and then data were collected for the following spontaneous cycles. An indwelling electrodeless plastic-coated toroidal conductivity sensor, which also recorded temperature, was placed in the vagina throughout the cycle. Blood samples were collected for LH measurement, and ultrasound scanning used to confirm ovulation. Although there was a relationship between vaginal mucus conductivity measured by the toroidal sensor and the timing of the LH surge, it was not sufficiently robust in individual cows to be able to identify the time of the LH surge. The mean increase in vaginal temperature at estrus was 0.48 degrees C. An algorithm was developed which used the detected individual cow temperature peak to test the relationship with the LH peak. In 16 out of 21 cases where ovulation was confirmed and data existed, the estimated individual peak was within 4h of the LH surge, in three cases it was +/-6h, and in two instances it was early. In conclusion, the temperature algorithm was able to identify the time of the LH surge and thus predict time of ovulation in a way that would allow effective AI, although this result needs to be tested in lactating cows. However, the toroidal conductivity sensing method was not able to produce data of sufficient quality to develop a predictive relationship in individual cows.
Asunto(s)
Temperatura Corporal/fisiología , Bovinos/fisiología , Conductividad Eléctrica , Hormona Luteinizante/sangre , Vagina/fisiología , Animales , Ciclo Estral/fisiología , Femenino , Ovulación/fisiología , Detección de la Ovulación/instrumentación , Detección de la Ovulación/métodos , Detección de la Ovulación/veterinariaRESUMEN
Controlling spatial positioning of cattle through use of electronic collars could provide new ways to farm under extensive conditions. This study examined the potential for bulls to be controlled during mating using mild electric shocks delivered through radio-controlled collars. Eighteen Belmont Red bulls were fitted with collars containing the Global Positioning System and that were able to emit a mild electric shock (500 mW) at the top of the neck behind the poll. Eighteen Belmont Red cows were fitted with Global Positioning System collars only. The experiment was replicated 3 times in 3 paddocks. Each paddock contained 2 bulls and 1 cow in induced estrus. On d 1, the bulls were either assigned to the cow or not assigned to the cow, and on d 2, the assignments were reversed, and bulls received the other treatment using a new cow. Treatments were applied for 2 h on each day. The nonassigned bull received a mild electric shock on approach to either the cow or to a bull, whereas the assigned bull received a mild electric shock on approach to the other bull only. The electric shock was applied when the bulls were within approximately 10 m and moving toward the nonallowed animal. The electric shock was terminated when the animal responded by stopping movement toward the nonallowed animal. In the first 10 min, nonassigned bulls spent less time within 5 m of the cow (P = 0.03) than assigned bulls. Assigned bulls spent more time close to the cow during the entire 120 min on d 1 than on d 2 (P = 0.014). On d 1, the assigned bulls moved more toward the cow and the nonassigned bull than they did on d 2 (P = 0.02). Assigned bulls displayed more sexual behaviors than nonassigned bulls (P = 0.004). Nonassigned bulls were sometimes observed not to approach the cow despite a change in its location. This suggests that the bull associated the electric shock with the cow and not with the location in which it received the electric shock. Instances were observed in which the cow pursued the nonassigned bull, in which case the bull did not receive an electric shock, and this may reflect the preference of the cow. This study demonstrated that bulls can be separated and prevented from approaching a cow in estrus using a mild electric shock. However, mate allocation was not completely successful due to the potential for cow preference for certain bulls.
Asunto(s)
Crianza de Animales Domésticos/métodos , Bovinos/fisiología , Conducta Sexual Animal , Animales , Femenino , Masculino , Proyectos Piloto , Distribución AleatoriaRESUMEN
Traditional methods of variance component estimation for traits under maternal influence consist of partitioning the variance into direct additive genetic, maternal additive genetic, permanent maternal environmental, and error variance components. This partitioning is based on the assumption that each calf is nurtured and fed exclusively by its own dam. However, under extensive pastoral systems, voluntary cross-suckling may occur and could be quantified by using contact loggers recording cow-calf affiliations. A simulation study was conducted to test several variance models for partitioning maternal variation by including information on cow-calf contacts. The results indicated that weighting maternal genetic and permanent maternal environmental effects by the relative time calves spent with particular cows, including their own mothers, is feasible and significantly increased the log-likelihood of the models. However, the interpretation of the variance components in terms of traditional direct and maternal heritability is no longer straightforward. The need for further research and implications for the industry are discussed.
Asunto(s)
Crianza de Animales Domésticos/métodos , Bovinos/genética , Variación Genética , Exposición Materna , Modelos Biológicos , Modelos Genéticos , Animales , Animales Recién Nacidos , Bovinos/crecimiento & desarrollo , Simulación por Computador , Femenino , Funciones de Verosimilitud , Masculino , DesteteRESUMEN
The number of eggs from gastrointestinal nematodes per gram of faeces (worm egg count WEC) is commonly used to determine the need for anti-parasite treatments and the breeding value of animals when selecting for worm resistance. Diarrhoea increases faecal moisture and may dilute the number of worm eggs observed. To quantify this effect, egg counts in sheep at pasture were simulated by dosing 15 animals with chromic oxide particles. The simulated WEC diminished as faecal moisture increased. When faeces were dried, simulated WEC per unit dry matter was not influenced by the amount of faecal moisture present prior to drying. The results suggest that adjustment for faecal moisture may provide an improved estimate of FEC. Drying faeces to calculate the WEC per unit dry matter would provide such an adjustment but may not be practical for industry application. In the past, the CSIRO McMaster Laboratory has used an adjustment factor developed by Gordon based on the classification of faecal consistency derived from the morphology of faeces. To examine the utility of an adjustment factor based on faecal consistency score (FCS), the relationships between FCS and simulated WEC and dry matter were examined. Dry matter and simulated WEC exhibited an exponential decline as FCS increased. The relationship between FCS and dry matter was further examined in 368 samples collected over 12 months from sheep at pasture, where it was observed that dry matter showed a linear decline as FCS increased. Adjustment factors based on dry matter were similar to those proposed by Gordon however adjustment factors predicted from simulated WEC diverged from the remainder for FCS>4. As no samples scored FCS 5 in the study of simulated FEC, the adjustment factors based on the larger study that included samples with FCS 5 was therefore considered more robust. Adjustment factors were given by the equation: WEC(estimated)=(WEC(observed)/(34.21-5.15 FCS))x29.06. This equation estimates for samples with FCS>1 the WEC that would be expected if the samples were FCS 1, the faecal consistency score for normal faeces. The impact of adjustment of observed WEC for faecal moisture predicted by FCS on decision points for treatment and on estimated breeding values requires further examination.
Asunto(s)
Heces/química , Heces/parasitología , Enfermedades de las Ovejas/diagnóstico , Tricostrongiloidiasis/veterinaria , Agua/química , Animales , Compuestos de Cromo/química , Recuento de Huevos de Parásitos/métodos , Recuento de Huevos de Parásitos/veterinaria , Ovinos , Tricostrongiloidiasis/diagnósticoRESUMEN
QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.
Asunto(s)
Algoritmos , Animales Domésticos/genética , Cruzamiento/métodos , Fenotipo , Sitios de Carácter Cuantitativo , Animales , Mapeo Cromosómico , Simulación por Computador , Femenino , Genotipo , Funciones de Verosimilitud , Desequilibrio de Ligamiento , Masculino , Modelos GenéticosRESUMEN
Methods for detecting Quantitative Trait Loci (QTL) without markers have generally used iterative peeling algorithms for determining genotype probabilities. These algorithms have considerable shortcomings in complex pedigrees. A Monte Carlo Markov chain (MCMC) method which samples the pedigree of the whole population jointly is described. Simultaneous sampling of the pedigree was achieved by sampling descent graphs using the Metropolis-Hastings algorithm. A descent graph describes the inheritance state of each allele and provides pedigrees guaranteed to be consistent with Mendelian sampling. Sampling descent graphs overcomes most, if not all, of the limitations incurred by iterative peeling algorithms. The algorithm was able to find the QTL in most of the simulated populations. However, when the QTL was not modeled or found then its effect was ascribed to the polygenic component. No QTL were detected when they were not simulated.
Asunto(s)
Algoritmos , Meiosis/genética , Carácter Cuantitativo Heredable , Alelos , Animales , Simulación por Computador , Femenino , Orden Génico , Genética de Población , Genotipo , Heterocigoto , Homocigoto , Masculino , Cadenas de Markov , Modelos Genéticos , Método de Montecarlo , LinajeRESUMEN
A method for estimating genotypic and identity-by-descent probabilities in complex pedigrees is described. The method consists of an algorithm for drawing independent genotype samples which are consistent with the pedigree and observed genotype. The probability distribution function for samples obtained using the algorithm can be evaluated up to a normalizing constant, and combined with the likelihood to produce a weight for each sample. Importance sampling is then used to estimate genotypic and identity-by-descent probabilities. On small but complex pedigrees, the genotypic probability estimates are demonstrated to be empirically unbiased. On large complex pedigrees, while the algorithm for obtaining genotype samples is feasible, importance sampling may require an infeasible number of samples to estimate genotypic probabilities with accuracy.
Asunto(s)
Algoritmos , Genotipo , Linaje , Frecuencia de los GenesRESUMEN
Experiments to map QTL usually measure several traits, and not uncommonly genotype only those animals that are extreme for some trait(s). Analysis of selectively genotyped, multiple-trait data presents special problems, and most simple methods lead to biased estimates of the QTL effects. The use of logistic regression to estimate QTL effects is described, where the genotype is treated as the dependent variable and the phenotype as the independent variable. In this way selection on phenotype does not bias the results. If normally distributed errors are assumed, the logistic-regression analysis is almost equivalent to a maximum-likelihood analysis, but can be carried out with standard statistical packages. Analysis of a simulated half-sib experiment shows that logistic regression can estimate the effect and position of a QTL without bias and confirms the increased power achieved by multiple-trait analysis.
Asunto(s)
Carácter Cuantitativo Heredable , Genotipo , Humanos , Modelos Logísticos , Fenotipo , Recombinación GenéticaRESUMEN
T-cell receptor antibodies (TCR alpha beta and TCR gamma delta) were used for a flow cytometric study of 114 specimens of lymphoid neoplasms and normal controls in order to find out whether or not the expression of TCR proteins differs in between normal and neoplastic tissues. It was found that TCR alpha beta population was predominant in all categories except T gamma lymphoproliferative disorder (TGLD), T-cell lymphoblastic leukemia (T-ALL), and natural killer-like T-cell lymphoma (NKTL), in which three of 18, one of three, and two of two specimens, respectively, showed a predominant TCR gamma delta population. Natural killer cell lymphoma (NKL) showed essentially absence of either TCR alpha beta or TCR gamma delta protein. Therefore, TCR antibodies can be selectively used in cases of TGLD, T-ALL, and NKTL to substantiate their diagnoses. Furthermore, the absence of TCR protein is characteristic of NKL and helps to distinguish it from NKTL. Without the TCR antibodies, TCR gene analysis is sometimes needed to separate these two entities. When comparing with genotyping, 11 of 12 cases with TCR beta gene rearrangement and one of two cases with TCR alpha gene rearrangement expressed TCR alpha beta protein. One of four cases with TCR gamma gene rearrangement and both cases with TCR delta gene rearrangement expressed TCR gamma delta protein. Thus, TCR antibody phenotyping can reliably predict TCR genotypes under most circumstances.
Asunto(s)
Expresión Génica , Genotipo , Linfoma/genética , Fenotipo , Receptores de Antígenos de Linfocitos T/genética , Diagnóstico Diferencial , Citometría de Flujo , Reordenamiento Génico de Linfocito T , Humanos , Inmunofenotipificación , Leucemia/diagnóstico , Leucemia/genética , Leucemia/inmunología , Leucemia Linfocítica Crónica de Células B/genética , Leucemia-Linfoma de Células T del Adulto/genética , Linfoma/diagnóstico , Linfoma/inmunología , Linfoma de Células B/genética , Linfoma de Células T/genéticaRESUMEN
Large granular T-cell lymphoproliferative disorder (LGTLD) is a heterogeneous disorder covering a broad spectrum of diseases and requiring further subdivision. Most reported cases emphasized its suppressor phenotype (T gamma cell or CD8+), but we encountered two cases of CD3+, CD4-, CD8- LGTLD. Both cases had a benign clinical course and required no chemotherapy despite persistent lymphocytosis. This unique phenotype has been reported in a few cases of acute lymphoblastic leukemia expressing the T-cell receptor (TcR) gamma chain gene and is considered the counterpart of thymocytes at the intermediate stage between early precursors and mature thymocytes. Our case 1 provides further evidence that the CD3+, CD4-, CD8- phenotype, indeed, expresses the TcR gamma chain gene. However, the negative reaction to terminal deoxynucleotidyl transferase in our case 1 indicates that this phenotype represents proliferation of peripheral T-cells, in which about 2% bear the CD3+, CD4-, CD8- phenotype in the normal population. The selective use of CD3, CD4, CD8, HNK-1 monoclonal antibodies and of cytochemical stains (acid phosphatase and alpha-naphthyl butyrate esterase) for characterization of this disorder is discussed.
Asunto(s)
Antígenos de Diferenciación de Linfocitos T/análisis , Antígenos CD4/análisis , Células Asesinas Naturales/inmunología , Trastornos Linfoproliferativos/inmunología , Receptores de Antígenos de Linfocitos T/análisis , Adulto , Anciano , Anciano de 80 o más Años , Complejo CD3 , Antígenos CD8 , Citometría de Flujo , Reordenamiento Génico de la Cadena beta de los Receptores de Antígenos de los Linfocitos T , Humanos , Inmunofenotipificación , MasculinoRESUMEN
It was shown by flow cytometry analysis that crystalized preparation of Cordyceps sinensis (Cs-Cr) caused significant elevation of the number of T helper cells and Lyt-1/Lyt-2 (T helper to T suppressor cell) ratio both in peripheral blood and the treated mice spleen. The spleen weight, phagocyte counts and phagocytic activity were also elevated in the treated group. In addition, Cs-Cr could protect T helper cells from the immunosuppressive effects of prednisolone acetate and cyclophosphamide. These results further substantiate the fact that Cs-Cr is an immunoregulator/biological response modifier of cellular immunity and may be potentially useful in handling immunodeficient or immunosuppressed patients.
Asunto(s)
Medicamentos Herbarios Chinos/farmacología , Factores Inmunológicos , Subgrupos de Linfocitos T/efectos de los fármacos , Animales , Femenino , Hypocreales , Lepidópteros , Recuento de Leucocitos , Masculino , Ratones , Ratones Endogámicos BALB C , Bazo/citología , Subgrupos de Linfocitos T/inmunología , Linfocitos T Colaboradores-Inductores/inmunología , Linfocitos T Reguladores/inmunologíaRESUMEN
Comparison of phenotyping (PT) and genotyping (GT) of lymphoid neoplasms was performed on 51 specimens including lymph nodes, bone marrows, and body fluids. PT was performed with a flow cytometer using a large monoclonal antibody panel. GT included the testing for gene rearrangements of heavy chain, kappa and lambda light chains, and T-cell receptor beta-chain genes with DNA probes. The results obtained from these two techniques were generally compatible in terms of clonality and cell lineage. Only one case of B-cell lymphoma was not diagnosed by PT but showed gene rearrangement. For T-cell lymphoma, GT offers a more definitive diagnosis than does PT. Biclonality was demonstrated in one case of hairy cell leukemia by GT only. The rearranged band also offers a definitive clonal identification based on electrophoretic mobility. GT can detect a monoclonal population as small as 5% and can be performed on old or fresh specimens. PT requires 20% abnormal cells and a fresh specimen. It is concluded that GT is superior to PT for lymphoid tumor diagnosis, but it should be reserved as a supplementary test at this stage because of its technical complexity.
Asunto(s)
Anticuerpos Monoclonales , Antígenos de Neoplasias/análisis , Biomarcadores de Tumor/análisis , ADN de Neoplasias/análisis , Reordenamiento Génico , Leucemia/diagnóstico , Linfoma/diagnóstico , Genotipo , Humanos , Leucemia/genética , Leucemia/inmunología , Linfoma/genética , Linfoma/inmunología , Fenotipo , Timoma/diagnóstico , Timoma/genética , Timoma/inmunologíaRESUMEN
Multimarker studies were conducted on 195 lymph node, 59 bone marrow, 44 peripheral blood, eight body fluid, and eight internal organ specimens. The markers were identified by fluorochrome-labeled antibodies quantified with flow cytometry. T-cell receptor gene rearrangements were used for the determination of T-cell clonality. These studies confirmed that CD 19 (B4, Leu 12) is highly sensitive for B-lymphoblastic leukemia, CD 7 (Leu 9) is highly sensitive for T-lymphoblastic leukemia, and CD 5 (Leu 1) is highly sensitive for chronic lymphocytic leukemia. When these markers were compared to antigens of the same cell lineage (e.g., CD 19 to CD 20 [Leu 16] or to surface immunoglobulin, CD 7 to CD 3 [Leu 4], and CD 5 to CD 3), a marked discrepancy between them was diagnostic of the corresponding tumor. T-cell marker discrepancy (CD3 vs. CD 7) was demonstrated in T-cell lymphomas, but it was also shown occasionally in polyclonal T-cell populations. On the other hand, a marked discrepancy between the percentages of a B-lineage (CD 19 or CD 20)-positive and a surface-immunoglobulin-positive population is a reliable phenotype for the diagnosis of a surface-immunoglobulin-negative B-cell lymphoma.