Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project

BACKGROUND

Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications.

MATERIALS AND METHODS

Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values.

RESULTS

Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples.

CONCLUSIONS

Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.

Abstract 4668: Evidence for antigen-driven TCRB chain convergence in the tumor infiltrating T cell repertoire of 85 research subjects with melanoma

Introduction

T cell convergence refers to the phenomenon whereby antigen-driven selection enriches for T cell receptors having a shared antigen specificity but different amino acid or nucleotide sequence. T cell recruitment and expansion within the tumor microenvironment (TME) may be directed by responses to tumor neoantigen, suggesting that elevated T cell convergence could be a general feature of the tumor infiltrating T cell repertoire. Here we evaluate evidence for T cell convergence within tumor biopsy research samples from a set of 85 subjects with melanoma.

Methods

Total RNA from 85 tumor biopsy research samples (non-FFPE) was extracted for use in long-amplicon TCRB chain sequencing (mean amplicon length of 330bp covering CDR1, 2 and 3) via the Ion AmpliSeq Immune Repertoire Assay Plus, TCRB. To evaluate T cell convergence within each biopsy, we searched for instances where TCRB chains were identical in amino acid space (shared variable gene identity and CDR3 amino acid sequence) but had distinct nucleotide sequences owing to N-addition and exonucleotide chewback within the V-D and D-J junctions of the CDR3. To provide context, we evaluated evidence for T cell convergence with T cell repertoires derived from healthy donor peripheral blood leukocytes (PBL).

Results

Sequencing of melanoma biopsies yielded an average of 6029 clones per sample. 11 of 85 samples yielded fewer than 100 clones and were eliminated from downstream analysis. Convergent T cell receptors were identified in 68/74 (92%) of tumor infiltrating T cell repertoires having greater than 100 detected clones. The frequency of convergent rearrangements was approximately 50-fold greater in the melanoma-infiltrating T cell repertoire than healthy PBL samples (p<.001).

Conclusions

These data suggest that T cell convergence may be a common feature of the melanoma infiltrating T cell repertoire. Convergence was more frequently observed within the TME than T cell repertoires derived from healthy PBL, consistent with elevated antigen-driven T cell selection within the TME. The extent to which convergence is a feature of the TME in other cancers is not yet known. T cell receptor convergence may be driven by T cell responses to tumor neoantigen within the TME. In such case, in silico identification of convergent T cell receptors by long-amplicon sequencing may serve as an approach for rapid identification of antigen-specific T cell receptors for future therapeutic use.

For research use only.

Citation Format: Timothy J. Looney, Sean Glenn, Sarabjot Pabla, Jeff Conroy, Carl Morrison, Alice Zheng, Lauren Miller, Elizabeth Linch, Denise Topacio, Geoff Lowman, Fiona Hyland, Mark Anderson. Evidence for antigen-driven TCRB chain convergence in the tumor infiltrating T cell repertoire of 85 research subjects with melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4668.

Comparative reliability and diagnostic performance of conventional 3T magnetic resonance imaging and 1.5T magnetic resonance arthrography for the evaluation of internal derangement of the hip

Objective

To compare the diagnostic accuracy of conventional 3T MRI against 1.5T MR arthrography (MRA) in patients with clinical femoroacetabular impingement (FAI).

Methods

Sixty-eight consecutive patients with clinical FAI underwent both 1.5T MRA and 3T MRI. Imaging was prospectively analysed by two musculoskeletal radiologists, blinded to patient outcomes and scored for internal derangement including labral and cartilage abnormality. Interobserver variation was assessed by kappa analysis. Thirty-nine patients subsequently underwent hip arthroscopy and surgical results and radiology findings were analysed.

Results

Both readers had higher sensitivities for detecting labral tears with 3T MRI compared to 1.5T MRA (not statistically significant p=0.07). For acetabular cartilage defect both readers had higher statistically significant sensitivities using 3T MRI compared to 1.5T MRA (p=0.02). Both readers had a slightly higher sensitivity for detecting delamination with 1.5T MRA compared to 3T MRI, but these differences were not statistically significant (p=0.66). Interobserver agreement was substantial to perfect agreement for all parameters except the identification of delamination (3T MRI showed moderate agreement and 1.5T MRA substantial agreement).

Conclusion

Conventional 3T MRI may be at least equivalent to 1.5T MRA in detecting acetabular labrum and possibly superior to 1.5T MRA in detecting cartilage defects in patients with suspected FAI.

Key Points

• Conventional 3T MRI is equivalent to 1.5T MRA for diagnosing labral tears.

• Conventional 3T MRI is superior to 1.5T MRA for diagnosing acetabular cartilage defect.

• Conventional 3T MRI is equivalent to 1.5T MRA for diagnosing cartilage delamination.

• Symptom severity score was significantly higher (p<0.05) in group proceeding to surgery.

Analytical validation of an immune response assay for classifying solid tumors

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Background: An advanced diagnostic laboratory test (Immune Advance) was developed that analyzes multiple DNA and RNA biomarkers to predict the likelihood of response to checkpoint inhibitors in patients with solid tumors. Using RNA-seq and DNA-seq, the NGS test measures gene expression of immune response genes and overall mutational burden. The studies described here were designed to validate the analytical performance of the test on the Ion Torrent System in our CLIA lab. Methods: Studies were designed to characterize the analytical performance of an immune response NGS assay using total nucleic acids from >100 FFPE tissues representing NSCLC, melanoma, renal cell carcinoma, and bladder cancer. Performance variables with respect to gene-specific amplicon specificity, linearity, and limits of detection were estimated with various sample dilutions and input nucleic acids. The effects of the tumor micro-environment (adjacent benign tissue, necrosis) was evaluated by including these potential interferents in the assay. Analytical precision including intra-assay, inter-assay, and inter-operator reproducibility was measured by testing replicate FFPE tissue sections. Accuracy was determined by comparing select transcript and DNA level variants with those from established IHC, RT-PCR, and NGS assays. Transcript stability in FFPE specimens was evaluated in serial sections from blocks with routine storage and compared to originating matched fresh frozen specimens. Results: RNA stability was demonstrated by high degree of correlation between matched frozen and FFPE samples. Analytic precision was demonstrated by high correlation between RNA-Seq and TaqMan results for genes evaluated. As compared to IHC the results for RNA-Seq were continuous rather than bimodal and allowed for a much more detailed analysis of the immune response. Immune signatures were maintained with variable RNA/DNA input amounts, altered tumor micro-environments, and potential interferents demonstrating tolerance to typical sample types tested. Reproducibility results show little variation between runs and operators. Conclusions: The analytical performance of the Immune Advance assay has been validated for clinical use using FFPE tumor specimens.

The use of the Hemochron in assessment of heparin reversal after cardiopulmonary bypass

The use of the Hemochron activated clotting time (ACT) for determining adequacy of reversal of heparin following cardiopulmonary bypass was evaluated in 20 patients and compared with standard laboratory tests of coagulation. The commonly used Celite ACT method proved too insensitive to have any useful predictive value in detecting or quantifying residual heparin and removal of the Celite activation rendered the test even less sensitive. In contrast, the partial thromboplastin time with kaolin (PTTK) proved to correlate well with residual heparin ( r = 0.79). It is, therefore, recommended that the use of the Hemochron following protamine administration be abandoned in favour of the PTTK.

NAPB - a novel SNARE-associated protein for early-onset epileptic encephalopathy

Next-generation sequencing has accelerated the identification of disease genes in many rare genetic disorders including early-onset epileptic encephalopathies (EOEEs). While many of these disorders are caused by neuronal channelopathies, the role of synaptic and related neuronal proteins are increasingly being described. Here, we report a 6-year-old girl with unexplained EOEE characterized by multifocal seizures and profound global developmental delay. Recessive inheritance was considered due to parental consanguinity and Irish Traveller descent. Exome sequencing was performed. Variant prioritization identified a homozygous nonsense variant in the N-ethylmaleimide-sensitive factor attachment protein, beta (NAPB) gene resulting in a premature stop codon and 46% loss of the protein. NAPB plays a role in soluble N-ethylmaleimide-sensitive fusion attachment protein receptor (SNARE)-complex dissociation and recycling (synaptic vesicle docking). Knockout mouse models of the murine ortholog Napb have been previously reported. These mice develop recurrent post-natal epileptic seizures in the absence of structural brain changes. The identification of a disease-causing variant in NAPB further recognizes the importance of the SNARE complex in the development of epilepsy and suggests that this gene should be considered in patients with unexplained EOEE.

Abstract P3-08-03: Defects in BRCA1 Contribute to Global Differential Allele-Specific Expression

Differential allele-specific expression (DASE) has been shown to contribute to phenotypic variability in humans and more recently to the pathogenesis of cancer. DASE is associated with X-chromosome inactivation and genomic imprinting and is relatively common among non-imprinted autosomal genes. The DASE phenotype can also be transmitted by Mendelian inheritance. We have previously reported that nonsense-mediated mRNA decay (NMD) of mutant BRCA1 as well as other epigenetic mechanisms can lead to DASE of BRCA1 and enhanced susceptibility to breast cancer. BRCA1 has been implicated in many cellular processes including DNA repair, cell-cycle-checkpoint control, protein ubiquitination, and chromatin remodeling. Importantly, cells carrying a deleterious BRCA1 mutation exhibit increased genome instability, therefore, we hypothesize that defects in BRCA1 lead not only to DASE of itself, but increase genome-wide DASE and thus contribute to increased breast cancer susceptibility. To test this hypothesis, we employed a genome-wide ASE assay (Illumina Human Omni1-Quad BeadChip) using primary mammary epithelial cells [3 BRCA1 wild-type vs. 3 BRCA1 mutant carrying (2800delAA, 4154delA and R1751X)]. As shown in Table 1, cells carrying a BRCA1 mutation had significantly more DASE events as compared to wild-type cell (P&lt;10-7). In addition, we identified 351 genes demonstrating DASE that were unique to the BRCA1 mutant cells. The cellular functions of these genes are wideranging, including DNA repair, cell cycle control, lipid metabolism and protein degradation. In summary, this study provides the first evidence that mutant BRCA1 can lead to global DASE, which in turn may contribute to the development of breast cancer in mutation carriers. This work was supported in part by the Eileen Stein-Jacoby Fund and a grant from the Congressionally Directed Medical Research Programs, Department of Defense, W81XWH-08-1-0361 (XC).

Table 1. BRCA1 mutations increase the global DASE in PMECs

t; A DASE event is defined as that the Log-ratio of allele-specific expression level of one gene is more than 1 or less than -1, i.e. the expression level from one allele is at least 50% less than the level of another allele

Vibrational spectroscopy for cervical cancer pathology, from biochemical analysis to diagnostic tool

Cervical cancer is the second most common cancer in women worldwide with 80% of cases arising in the developing world. The mortality associated with cervical cancer can be reduced if this disease is detected at the early stages of development or at the pre-malignant state (cervical intraepithelial neoplasia, CIN). The aim of this study was to investigate the potential of Raman spectroscopy as a diagnostic tool to detect biochemical changes accompanying cervical cancer progression. Raman spectra were acquired from proteins, nucleic acids, lipids and carbohydrates in order to gain an insight into the biochemical composition of cells and tissues. Spectra were also obtained from histological samples of normal, CIN and invasive carcinoma tissue from 40 patients. Multivariate analysis of the spectra was carried out to develop a classification model to discriminate normal from abnormal tissue. The results show that Raman spectroscopy displays a high sensitivity to biochemical changes in tissue during disease progression resulting in an exceptional prediction accuracy when discriminating between normal cervical tissue, invasive carcinoma and cervical intraepithelial neoplasia (CIN). Raman spectroscopy shows enormous clinical potential as a rapid non-invasive diagnostic tool for cervical and other cancers.

Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York

High-resolution array comparative genomic hybridisation (aCGH) analysis of DNA copy number aberrations (CNAs) was performed on breast carcinomas in premenopausal women from Western New York (WNY) and from Gomel, Belarus, an area exposed to fallout from the 1986 Chernobyl nuclear accident. Genomic DNA was isolated from 47 frozen tumour specimens from 42 patients and hybridised to arrays spotted with more than 3000 BAC clones. In all, 20 samples were from WNY and 27 were from Belarus. In total, 34 samples were primary tumours and 13 were lymph node metastases, including five matched pairs from Gomel. The average number of total CNAs per sample was 76 (range 35–134). We identified 152 CNAs (92 gains and 60 losses) occurring in more than 10% of the samples. The most common amplifications included gains at 8q13.2 (49%), at 1p21.1 (36%), and at 8q24.21 (36%). The most common deletions were at 1p36.22 (26%), at 17p13.2 (26%), and at 8p23.3 (23%). Belarussian tumours had more amplifications and fewer deletions than WNY breast cancers. HER2/neu negativity and younger age were also associated with a higher number of gains and fewer losses. In the five paired samples, we observed more discordant than concordant DNA changes. Unsupervised hierarchical cluster analysis revealed two distinct groups of tumours: one comprised predominantly of Belarussian carcinomas and the other largely consisting of WNY cases. In total, 50 CNAs occurred significantly more commonly in one cohort vs the other, and these included some candidate signature amplifications in the breast cancers in women exposed to significant radiation. In conclusion, our high-density aCGH study has revealed a large number of genetic aberrations in individual premenopausal breast cancer specimens, some of which had not been reported before. We identified a distinct CNA profile for carcinomas from a nuclear fallout area, suggesting a possible molecular fingerprint of radiation-associated breast cancer.

Serotonin transporter gene and autism: a haplotype analysis in an Irish autistic population

The role of the serotonin transporter (5-HTT) in the development of neuropsychiatric disorders has been widely investigated. Two polymorphisms, an insertion/deletion in the promoter region and a 12 repeat allele in a variable nucleotide tandem repeat (VNTR) in intron 2, drive higher expression of the 5-HTT gene. Four studies have shown nominally significant excess transmission of alleles of the 5-HTT gene in autism, while three studies have reported no excess transmission. This present study investigates the role of 5-HTT in the genetically homogenous Irish population. In all, 84 families were genotyped for five polymorphisms (three SNPs, a VNTR and an in/del). The analysis of allele transmissions using the transmission disequilibrium test (TDT) was undertaken and indicated preferential transmission of the short promoter allele (TDT P-value=0.0334). Linkage disequilibrium between markers was calculated and haplotypes were assessed for excess transmission and odds ratios (ORs) to affected children. A number of haplotypes, especially those involving and surrounding SNP10, showed evidence of association. The ORs ranged from 1.2 to 2.4. The most significant haplotype associated with transmission to affected probands was the SNP10-VNTR-SNP18 haplotype (chi(2)=7.3023, P=0.0069, odds ratio=1.8). This haplotype included the 12 repeat allele of the VNTR, which is associated with increased expression and may play a subtle role in the early development of the brain in affected probands.

Identification and characterisation of constitutional chromosome abnormalities using arrays of bacterial artificial chromosomes

Constitutional chromosome deletions and duplications frequently predispose to the development of a wide variety of cancers. We have developed a microarray of 6000 bacterial artificial chromosomes for array-based comparative genomic hybridisation, which provides an average resolution of 750 kb across the human genome. Using these arrays, subtle gains and losses of chromosome regions can be detected in constitutional cells, following a single overnight hybridisation. In this report, we demonstrate the efficiency of this procedure in identifying constitutional deletions and duplications associated with predisposition to retinoblastoma, Wilms tumour and Beckwith–Wiedemann syndrome.

Isolated rupture of the popliteus tendon in a professional soccer player

We report an unusual case of an isolated intra-substance rupture of the popliteus tendon in a professional soccer player. The injury, sustained in a soccer tackle, was diagnosed on magnetic resonance imaging and subsequently confirmed on arthroscopic examination of the knee. The impinging proximal stump was debrided and the patient returned to playing competitive soccer within 6 weeks of surgery.

Early internal fixation and soft tissue cover of severe open tibial pilon fractures

We studied 32 consecutive patients with open distal tibial pilon fractures. All patients had radical debridement with immediate skeletal stabilisation and early soft-tissue cover with a vascularized muscle flap. The minimum follow-up was 1 (range 1-8) year. There were four superficial infections, two deep infections and two amputations. There were no long-term problems with union and no patient required an ankle fusion. Patients were assessed using the SF-36 questionnaire. There were significant differences from the US norm in physical function score ( p<0.01), role physical score ( p<0.05) and physical component score ( p<0.01). Physical component score of 38.5 was significantly better ( p<0.01) when compared with amputees from severe lower-extremity trauma. Our protocol for management resulted in a good functional outcome with low infection and amputation rates.

Assembly of microarrays for genome-wide measurement of DNA copy number

We have assembled arrays of approximately 2,400 BAC clones for measurement of DNA copy number across the human genome. The arrays provide precise measurement (s.d. of log2 ratios=0.05-0.10) in cell lines and clinical material, so that we can reliably detect and quantify high-level amplifications and single-copy alterations in diploid, polyploid and heterogeneous backgrounds.

Dissemination and adoption of the Child and Adolescent Trial for Cardiovascular Health (CATCH): a case study in Texas

The total impact of a health promotion program can be measured by the efficacy of the intervention multiplied by the extent of its implementation across the target population. The Child and Adolescent Trial for Cardiovascular Health (CATCH) was a school-based health promotion project designed to decrease fat, saturated fat, and sodium in children's diets, increase physical activity, and prevent tobacco use. This article describes the dissemination of CATCH in Texas, including the theoretical framework, strategies used, and lessons learned. To date (Fall 2000), CATCH materials have been adopted by more than 728 elementary schools in Texas.

Integration of cytogenetic landmarks into the draft sequence of the human genome

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

Genome-wide allelotyping indicates increased loss of heterozygosity on 9p and 14q in early age of onset colorectal cancer

Colorectal cancer remains a significant public health challenge, despite our increased understanding of the genetic mechanisms involved in the initiation and progression of this disorder. It has become clear that multiple mechanisms lead to the tumorigenic phenotype, with familial predisposition syndromes accounting for less than 15% of all colorectal cancers. A genome-wide scan for loss of heterozygosity (LOH) was carried out with 150 highly polymorphic markers in an effort to identify additional loci involved in colorectal tumorigenesis in DNA samples from 42 colorectal cancer patients. The results confirm earlier observations that tumor DNAs from patients with hereditary nonpolyposis colon cancer (HNPCC) either maintain heterozygosity or exhibit altered or additional alleles. DNAs from patients with early onset colorectal carcinomas (diagnosed prior to age 50) revealed a higher overall degree of LOH than DNAs from patients with sporadic colorectal cancers diagnosed later in life (after age 50). While regions on 1p, 10q and 14q are suggestive, statistical analysis of LOH at these regions failed to reach significance. However, LOH at 9p did reveal a statistically significant increase in the early onset patient group, compared to the greater than age 50 group. LOH on 9p may involve inactivation of p16/CDKN2 through aberrant DNA methylation on the remaining chromosome, resulting in a situation analogous to a homozygous deletion of p16 and providing a selective growth advantage to these cells. This marker may prove to be a useful prognostic indicator for patient stratification in the design of therapy for early onset colorectal cancer patients.

Satisfaction of children in out-of-home care

A randomly selected sample of 1,100 children in out-of-home care in Illinois from 1993 to 1996 were interviewed in person regarding their satisfaction with the homes in which they lived and with their caregivers. They were also asked whether they felt loved and safe, and rated the quality of their lives before and after placement into care. The children rated their satisfaction with their living arrangements and with their caregivers as high, especially those who had lived in family foster care.

Measuring the consumer satisfaction of class members of a law suit

The present article describes a study of consumer satisfaction in a group of class members who are part of a mental disability law reform suit Consumer satisfaction was considered one aspect of compliance with this lawsuit. The class members have a primary diagnosis of intellectual disability, and in most cases, a secondary diagnosis of mental illness. Conducting consumer satisfaction studies among people with intellectual disabilities is often challenging because some of these consumers have difficulty articulating their needs and concerns. An interview schedule with simple quantitative and qualitative satisfaction questions was used. The present study investigated the satisfaction of a subgroup of these class members prior to and after having a court-supported service plan. The results reveal that these consumers became considerably more satisfied, and many of their specific satisfactions and dissatisfaction were identified. The results suggest that both quantitative and qualitative consumer responses can be helpful in determining compliance with court issues.

Use of psychotropic medications for persons with mental retardation who live in Oklahoma nursing homes

OBJECTIVE

The study examined the use of psychotropic medications to treat persons with mental retardation living in nursing homes in Oklahoma.

METHODS

Data were gathered on all 1,056 individuals funded through the Oklahoma mental retardation service system in 1995 to live in nursing homes. The Developmental Disabilities Quality Assurance Questionnaire was used to assess adaptive behavior, living site conditions, health, use of medications, and other variables.

RESULTS

The most frequently used class of psychotropic medications was antipsychotic medication, used by 31.8 percent of subjects. Sixteen percent received anxiolytic medication, and 6.1 percent received antidepressant medication. Stepwise multiple regression analysis indicated that use of antipsychotic medication was marginally predictable (less than 15 percent of the variance was explained) with a linear combination of six variables: mental health problems; violence toward others; adaptive behavior; screaming, yelling, or crying behavior; hyperactivity; and age.

CONCLUSIONS

A relatively high percentage of subjects received various forms of psychotropic medications, especially antipsychotics. The presence of behavior problems or mental health problems did not sufficiently explain the high rate of use of antipsychotic medication. The risks of this type of medication and its lower rate of use in group homes raise the question of the appropriateness of placing persons with mental retardation in nursing homes as they are currently conceived.

A consumer satisfaction survey of people with mental retardation and mental illness

This study investigated consumer satisfaction among 98 members of the Thomas S. class action lawsuit in North Carolina, in which the court ordered implementation of habilitative and residential service plans. Class members have mental retardation, and most also have a mental illness. Before the court order, 83 of the consumers were inappropriately placed in state psychiatric hospitals; one year after, 82 were living in community residences. A survey at baseline and one year later indicated that consumers' satisfaction had increased significantly. They were more satisfied with where they lived, the food, and the level of freedom. They also felt that staff were more helpful, and that more staff were "nice" rather than "mean."

Structure and evolution of teleost mitochondrial control regions

We amplified and sequenced the mitochondrial control region from 23 species representing six families of teleost fish. The length of this segment is highly variable among even closely related species due to the presence of tandemly repeated sequences and large insertions. The position of the repetitive sequences suggests that they arise during replication both near the origin of replication and at the site of termination of the D-loop strand. Many of the conserved sequence blocks (CSBs) observed in mammals are also found among fish. In particular, the mammalian CSB-D is present in all of the fish species studied. Study of potential secondary structures of RNAs from the conserved regions provides little insight into the functional constraints on these regions. The variable structure of these control regions suggests that particular care should be taken to identify the most appropriate segment for studies of intraspecific variation.

Virologic, immunologic, and clinical evaluation of human immunodeficiency virus antibody status of symptom-free children born to infected mothers

STUDY OBJECTIVE

To determine the prevalence of infection by the human immunodeficiency virus (HIV) in a population of symptom-free children who were born to HIV-infected mothers and who subsequently underwent seroreversion from an HIV antibody-positive to an HIV antibody-negative status.

DESIGN

Cohort.

SETTING

Pediatric HIV program in a community setting.

PATIENTS

We used HIV DNA polymerase chain reaction (PCR) and coculture to detect the presence or absence of HIV in peripheral blood mononuclear cells of 134 children aged 6 to 53 months. All children had HIV antibody at birth and underwent a subsequent seroreversion to antibody-negative status.

RESULTS

In 134 children with HIV antibody-negative status, 219 of 220 culture results and 242 of 247 HIV-1 DNA PCR assay results were negative. Six positive laboratory results were obtained for six different children, each of whom had negative results on multiple assays. For HIV-infected children, 56 of 62 cultures and 99 of 104 PCR evaluations showed positive results. There was no clinical or laboratory evidence of HIV infection in the group with HIV antibody-negative status.

CONCLUSION

We were unable to find evidence of latent HIV type 1 infection in this cohort of symptom-free children who underwent seroreversion to HIV antibody-negative status. The loss of maternal HIV antibody in these children indicates the absence of HIV infection. False-positive PCR and culture results occurred sporadically, indicating that repeated analysis of HIV seropositivity in infants and children is necessary.

Carnitine palmitoyl transferase deficiency in malignant hyperthermia

The activity of carnitine palmitoyl transferase, an enzyme that catalyzes the transport of long-chain acylcarnitines into mitochondria, was quantitated in EB-virus-transformed lymphoblasts from 7 patients with susceptibility for malignant hyperthermia. Immunoreactive enzyme protein was also measured using an enzyme-linked immunosorbent assay. Cell lines derived from patients with carnitine palmitoyl transferase deficiency of muscle and from normal individuals were used as positive and negative controls, respectively. One patient with malignant hyperthermia had a deficiency in the enzyme activity which was comparable with that of the known carnitine palmitoyl transferase deficient patients. This individual's lymphoblasts were also deficient in immunoreactive enzyme protein. All of the remaining patients with malignant hyperthermia were deficient only when the backward assay for carnitine palmitoyl transferase was used for quantitation. It is likely that a subset of individuals with a malignant hyperthermia phenotype have a primary deficiency of carnitine palmitoyl transferase and that others have a milder enzyme deficiency secondary to the primary defect in malignant hyperthermia.

A novel polymerase chain reaction method for detection of human immunodeficiency virus in dried blood spots on filter paper

A method for detection of proviral human immunodeficiency virus DNA in dried blood spots on filter paper by direct polymerase chain reaction (PCR) has been developed. To develop the method, a standard system was used which was prepared from cells each containing a single integrated provirus and titrated with normal donor blood. This rapid procedure provides virtually quantitative yields of nuclear DNA and exploits most of the standard methodology described for blood specimens. A nested PCR using SK38-SK39 gag as the internal primer pair was also designed; this PCR detected a single copy of provirus per filter at near theoretical frequency with SK19 probe. The utility of the procedure was demonstrated with clinical specimens. Blood spot filters from human immunodeficiency virus-infected and uninfected individuals were readily and unequivocally discriminated. The method is designed for ultimate use with large (1.5-ml) sample preparation tubes that are compatible as PCR tubes with thermal cyclers. This will permit convenient, direct single-tube PCR of dried blood specimens on filters. It should be adaptable to analysis of dried blood spots for a variety of infectious or genetic diseases.

Influence of host environment on growth of clonal CD5+B (Lyl+B) cells

Autoimmune NZB mice have increased percentages of CD5+B (Lyl+B) cells in both the spleen and peritoneum. We have previously reported that as NZB mice age they develop a clonal population of hyperdiploid CD5+B cells in the spleen. These cells can readily be transplanted into unirradiated recipients. The growth characteristics of such transplanted hyperdiploid NZB spleen cells were examined in different recipient strains to determine if the immunological status of the host environments affected the growth of the clonal CD5+B cells. Young NZB and NZB.xid recipients (lacking hyperdiploid CD5+B cells) allowed growth and expansion of unpassaged CD5+B cells derived from primary NZB mice. Similarly, (NZBxDBA/2) and (NZBxBALB/c) F1 recipients allowed for expansion of CD5+B cell clones from primary sources. In a separate experiment, T cell-depleted NZB spleen cells containing a hyperdiploid CD5+B cell clone were transferred to SCID mice. The SCID environment supported the growth of the primary clone. None of these recipients normally have elevated CD5+B cells, yet these recipients allowed growth of primary transferred hyperdiploid cells. However, a difference in the ability of these recipient strains in their ability to expand multiply passaged CD5+B cell clones was observed. These results indicate that while hyperdiploid CD5+B cells are difficult to be maintained in culture, they can readily be passaged in vivo. The host environment may provide growth factors or signals for endogenous growth factors. Although the CD5+B clones arise initially in a hyperactive autoimmune environment, a hyperimmune environment is not necessary to support their growth. Transferred CD5+B cells affect the recipient environment and reduce the percentages of normal B cells.