Diagnostic Phenotypes Research Articles

Comparison of diagnostic and relapse flow cytometry phenotypes in childhood acute lymphoblastic leukemia: Implications for residual disease detection: A report from the children's oncology group

Flow cytometric analysis of minimal residual disease (MRD) depends on detecting phenotypically abnormal populations. However, little is known about how phenotypic shifts between diagnosis and relapse affect MRD detection in childhood acute lymphoid leukemia (ALL). We compared diagnostic and relapse bone marrow specimens in 42 children with precursor B-ALL studied with the two-tube panel CD19-APC/CD45-PerCP/CD10-PE/CD20-FITC and CD19-APC/CD45-PerCP/CD9-PE/CD34-FITC. At least 29 cases had phenotypic shifts of intensity or coefficient of variation of distribution of one or more markers. Shifts were complex and could not be explained by change in maturation stage. In the majority of cases MRD populations more closely resembled the diagnostic than the relapse specimen. In 6 of 7 MRD negative cases we did not identify an abnormal population that resembled diagnosis or relapse. In the remaining case, in which CD34 and CD10 were lost between diagnosis and relapse, it is possible that we could have missed an MRD population resembling relapse. Phenotypic shifts are common, but do not affect MRD recognition. At most 1 of 42 cases might have harbored an abnormal population undetected because of shift. However, MRD analysis with rigid gating (looking strictly for abnormal phenotypes at diagnosis) might have missed many positive cases, 8 of 22 (36%) in this series.

Comparison of Diagnostic and Relapse Flow Cytometry Phenotypes in Childhood ALL: Implications for Residual Disease (MRD) Detection.

Flow cytometric analysis of MRD depends on detecting phenotypically abnormal populations. Phenotypic shifts are known to occur but there is little information to indicate how these shifts affect detection of MRD. We compared diagnostic and relapse bone marrow specimens in 36 children with precursor B-ALL studied with the two-tube panel CD19-APC/CD45-PerCP/CD10-PE/CD20-FITC and CD19/45/9/34 (Leukemia 13:558,1999). Small phenotypic shifts of either intensity or coefficient of variation of the distribution of at least one marker were seen in 34 cases, while 7 cases had shifts of 4 or more markers. Phenotypic shifts were complex and could not be explained simply by a change in maturation stage. CD19 was the most stable marker, changing in only 8 cases, CD45 changed in 10; CD10 in 13; CD9 in 14; CD20 in 16 and CD34 in 18. CD10 and CD20 generally lost intensity while CD45 mostly increased. CD34 changed from positive to negative (5 cases) or relapsed as the CD34-negative component when the diagnostic sample was partially positive (9 cases). In 26 cases there was a sufficient change in phenotype from diagnosis to relapse to determine if day 28 MRD more closely resembled the initial diagnostic or the subsequent relapse sample. In 13/19 MRD+ cases the day 28 phenotype resembled the diagnostic specimen and in 6 it resembled relapse. Surprisingly, time to relapse was similar in both groups. In 6 of the 7 MRD negative cases, retrospective review of the data did not identify an abnormal population that resembled either diagnosis or relapse. In the remaining case, in which both CD34 and CD10 were lost from diagnosis to relapse, it is possible that a MRD population resembling relapse might have been missed. We conclude that phenotypic shifts between diagnostic and relapse specimens in childhood ALL are relatively common, but that in general they do not interfere with the ability to recognize MRD. However, MRD analysis that adheres to rigid gating looking only for the precise abnormal phenotype seen at diagnosis might miss some positive cases.

The University of California, San Francisco Family Alcoholism Study. I. Design, Methods, and Demographics

The University of California, San Francisco (UCSF) Family Alcoholism Study is a project designed to identify genetic loci that influence susceptibility to alcohol dependence and related phenotypes. Evidence supports a substantial genetic contribution to alcoholism susceptibility. However, the genetic epidemiology of alcoholism is complex, and its clinical manifestation is heterogeneous, making phenotype definition and demonstration of linkage difficult. Despite these challenges, some progress has been made toward identifying genes. The UCSF Family Alcoholism Study used a small family design, focusing primarily on sibling pairs and parent-child trios for linkage and association studies. Alcoholism-related phenotypes were assessed through interview and self-report questionnaires, with a focus on unidimensional and subphenotypical traits. Data-driven approaches to determining the most promising phenotypes for genetic analysis are being used. Both genome-wide scan and candidate gene approaches were used. The study enrolled 2154 individuals from 970 families from December 1995 through January 2003. Test-retest and interrater reliability for clinical data are very good, and power estimates suggest that this study will have adequate power by linkage analysis to detect loci with moderate effects. Design, methods, and sample demographics of the UCSF Family Study are presented, along with intrafamilial correlations for primary diagnostic phenotypes. Plans for genetic analysis, novel approaches to phenotype refinement, and the implications of ascertainment bias for heritability estimates are discussed.

Endophenotypes as quantitative risk factors for psychiatric disease: Rationale and study design

Genetic influences on psychiatric disorders are well established. However, localization of the genes responsible for these effects has proved extremely difficult. One emerging strategy that may circumvent some of these difficulties is the use of quantitative risk factors, or endophenotypes, which are correlated with disease and may be closer to underlying genetic liability and to gene action than are diagnostic phenotypes. Genetic studies of quantitative endophenotypes require different sampling and analysis strategies than studies of disease state. The rationale for using quantitative risk factors as indicators of disease liability and the optimal study design for localizing genes influencing such risk factors are discussed. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 105:42–44, 2001. © 2001 Wiley-Liss, Inc.

Endophenotypes as quantitative risk factors for psychiatric disease: Rationale and study design

Genetic influences on psychiatric disorders are well established. However, localization of the genes responsible for these effects has proved extremely difficult. One emerging strategy that may circumvent some of these difficulties is the use of quantitative risk factors, or endophenotypes, which are correlated with disease and may be closer to underlying genetic liability and to gene action than are diagnostic phenotypes. Genetic studies of quantitative endophenotypes require different sampling and analysis strategies than studies of disease state. The rationale for using quantitative risk factors as indicators of disease liability and the optimal study design for localizing genes influencing such risk factors are discussed.

Familial aggregation of dyslexia phenotypes.

There is evidence for genetic contributions to reading disability, but the phenotypic heterogeneity associated with the clinical diagnosis may make identification of the underlying genetic basis difficult. In order to elucidate distinct phenotypic features that may be contributing to the genotypic heterogeneity, we assessed the familial aggregation patterns of Verbal IQ and 24 phenotypic measures associated with dyslexia in 102 nuclear families ascertained through probands in grades 1 through 6 who met the criteria for this disorder. Correlations between relatives were computed for all diagnostic phenotypes, using a generalized estimating equation (GEE) approach. GEE is a recently developed semiparametric method for handling correlated data. The method is robust to model misspecification and flexible in adjusting for the subjects' characteristics and pedigree sizes as well as for the ascertainment process, while estimating the correlations between related subjects. The Nonword Memory (NWM) subtest of a prepublication version of the Comprehensive Test of Phonological Processing (CTOPP) and Phonemic Decoding Efficiency (PDE) subtest of a prepublication version of the Test of Word Reading Efficiency (TOWRE) showed correlation patterns in relatives that are strongly supportive of a genetic basis. The Wechsler Scale Digit Span, the Word Attack subtest of the Woodcock Reading Mastery Test--Revised, and the Spelling subtest of the Wide Range Achievement Test--Third Edition had slightly weaker evidence of a genetic basis. Five additional phenotypes (the Spelling subtest of the Wechsler Individual Achievement Test, the Accuracy, Rate, and Comprehension subtests of the Gray Oral Reading Test--Third Edition, and Rapid Automatized Naming of Letters and Numbers) gave suggestive evidence of such a pattern. The results cross-validate in that evidence for a pattern consistent with a genetic basis was obtained for two measures of phonological short-term memory (CTOPP Nonword Memory and WISCIII or WAIS-R Digit Span), for two measures of phonological decoding (WRMT-R Word Attack and TOWRE Phonemic Decoding Efficiency), and for two measures of spelling from dictation (WRAT-3 Spelling and, to a lesser extent, WIAT Spelling). These measures are thus good candidates for more sophisticated segregation analyses that can formulate models for incorporation into linkage analyses.

Molecular analysis of Sindbis virus pathogenesis in neonatal mice by using virus recombinants constructed in vitro.

Genetic loci affecting Sindbis virus pathogenesis in neonatal mice have been examined by using a full-length cDNA clone of the virus (Toto1101). The full-length cDNA is linked to a bacteriophage SP6 promoter to facilitate the synthesis of infectious RNA transcripts in vitro. Virus derived from Toto1101 showed reduced virulence (attenuation) in neonatal mice. Replacement of the E1 glycoprotein and 6K genes of Toto1101 with cloned E1 and 6K genes derived from a virulent Sindbis virus strain, AR339 (SB), resulted in a new construct, TR2000, that gave rise to virulent virus. Sequence determinations for the entire substituted regions of TR2000, Toto1101, and related virulent and attenuated strains identified three coding differences in E1 between Toto1101 and TR2000. These differences, individually or in combination, may be responsible for the attenuated phenotype. Previous studies in this laboratory identified another attenuating mutation at amino acid position 114 of the E2 glycoprotein (N.L. Davis, F.J. Fuller, W.G. Dougherty, R.A. Olmsted, and R.E. Johnston, Proc. Natl. Acad. Sci. USA 83:6771-6775, 1986). Substitution of Arg-114 in the mutant SB-RL for Ser-114 of SB appears to confer three distinguishing phenotypes: attenuation in neonatal mice, increased sensitivity to specific E2 monoclonal antibodies, and accelerated penetration of BHK cells. Replacement of TR2000 sequences containing the codon for amino acid 114 of E2 with corresponding fragments from cDNA clones of SB or SB-RL produced two strains of Sindbis virus (TR2100 and TR2200) which were isogenic except for the E2 114 codon (Ser and Arg, respectively). The three diagnostic phenotypes cosegregated according to the origin of the codon for amino acid 114 of E2, confirming the dramatic effect of this single amino acid substitution on these three phenotypes.

Spectrum of Susceptibility to Malignant Hyperthermia-Diagnostic Dilemma

Utilizing established in vitro muscle contracture tests, we have identified three diagnostic contracture phenotypes for malignant hyperthermia susceptibility (MHS) among 103 patients. Phenotype H is an unequivocal diagnostic result for MHS, as is the nonsusceptible phenotype N. The third diagnostic group, phenotype K, represents an equivocal diagnostic response. To provide a basis for understanding relationships between contracture phenotypes and MHS, pigs with phenotypes H, K, and N were exposed to a standardized anesthetic protocol for assessing MHS. During the anesthetic challenge, phenotype H pigs developed a more severe form of the MH syndrome than did phenotype K pigs. Comparing phenotype H v K average responses, VO2 increased four- v twofold; lactate increased 13- v 9-fold; and temperature increased 41.7 degrees C v 39.2 degrees C, respectively. These values either had no change or decreased in the phenotype N pigs. Results of this study suggest that a spectrum of MHS exists among the human population.

Spectrum of Susceptibility to Malignant Hyperthermia???Diagnostic Dilemma

Utilizing established in vitro muscle contracture tests, we have identified three diagnostic contracture phenotypes for malignant hyperthermia susceptibility (MHS) among 103 patients. Phenotype H is an unequivocal diagnostic result for MHS, as is the nonsusceptible phenotype N. The third diagnostic group, phenotype K, represents an equivocal diagnostic response. To provide a basis for understanding relationships between contracture phenotypes and MHS, pigs with phenotypes H, K, and N were exposed to a standardized anesthetic protocol for assessing MHS. During the anesthetic challenge, phenotype H pigs developed a more severe form of the MH syndrome than did phenotype K pigs. Comparing phenotype H v K average responses, Vo2 increased four- v twofold; lactate increased 13− v 9-fold; and temperature increased 41.7°C v 39.2°C, respectively. These values either had no change or decreased in the phenotype N pigs. Results of this study suggest that a spectrum of MHS exists among the human population.