The OGCleaner: filtering false-positive homology clusters

Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies.

AVAILABILITY AND IMPLEMENTATION

https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.

A novel approach for multi-SNP GWAS and its application in Alzheimer's disease

BACKGROUND

Genome-wide association studies (GWAS) have effectively identified genetic factors for many diseases. Many diseases, including Alzheimer's disease (AD), have epistatic causes, requiring more sophisticated analyses to identify groups of variants which together affect phenotype.

RESULTS

Based on the GWAS statistical model, we developed a multi-SNP GWAS analysis to identify pairs of variants whose common occurrence signaled the Alzheimer's disease phenotype.

CONCLUSIONS

Despite not having sufficient data to demonstrate significance, our preliminary experimentation identified a high correlation between GRIA3 and HLA-DRB5 (an AD gene). GRIA3 has not been previously reported in association with AD, but is known to play a role in learning and memory.

Detecting false positive sequence homology: a machine learning approach

Background

Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. There are many existing heuristic tools, most commonly based on bidirectional BLAST searches that are used to identify homologous genes and combine them into two fundamentally distinct classes: orthologs and paralogs. Due to only using heuristic filtering based on significance score cutoffs and having no cluster post-processing tools available, these methods can often produce multiple clusters constituting unrelated (non-homologous) sequences. Therefore sequencing data extracted from incomplete genome/transcriptome assemblies originated from low coverage sequencing or produced by de novo processes without a reference genome are susceptible to high false positive rates of homology detection.

Results

In this paper we develop biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes. We demonstrate that our machine learning method trained on both known homology clusters obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determines apparent false positives inferred by heuristic algorithms especially among proteomes recovered from low-coverage RNA-seq data. Almost ~42 % and ~25 % of predicted putative homologies by InParanoid and HaMStR respectively were classified as false positives on experimental data set.

Conclusions

Our process increases the quality of output from other clustering algorithms by providing a novel post-processing method that is both fast and efficient at removing low quality clusters of putative homologous genes recovered by heuristic-based approaches.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-0955-3) contains supplementary material, which is available to authorized users.

ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction

MOTIVATION

The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions.

RESULTS

Our results suggest that our greedy heuristic algorithm not only works well but also outperforms the other algorithms due to the nature of scaffold graphs. Our results also demonstrate a novel method for identifying inverted repeats and inversion variants, both of which contradict the basic single-orientation assumption. Such inversions have previously been noted as being difficult to detect and are directly involved in the genetic mechanisms of several diseases.

AVAILABILITY AND IMPLEMENTATION

http://bioresearch.byu.edu/scaffoldscaffolder.

CONTACT

paulmbodily@gmail.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Effects of error-correction of heterozygous next-generation sequencing data

Background

Error correction is an important step in increasing the quality of next-generation sequencing data for downstream analysis and use. Polymorphic datasets are a challenge for many bioinformatic software packages that are designed for or assume homozygosity of an input dataset. This assumption ignores the true genomic composition of many organisms that are diploid or polyploid. In this survey, two different error correction packages, Quake and ECHO, are examined to see how they perform on next-generation sequence data from heterozygous genomes.

Results

Quake and ECHO perform well and were able to correct many errors found within the data. However, errors that occur at heterozygous positions had unique trends. Errors at these positions were sometimes corrected incorrectly, introducing errors into the dataset with the possibility of creating a chimeric read. Quake was much less likely to create chimeric reads. Quake's read trimming removed a large portion of the original data and often left reads with few heterozygous markers. ECHO resulted in more chimeric reads and introduced more errors than Quake but preserved heterozygous markers.

Using real E. coli sequencing data and their assemblies after error correction, the assembly statistics improved. It was also found that segregating reads by haplotype can improve the quality of an assembly.

Conclusions

These findings suggest that Quake and ECHO both have strengths and weaknesses when applied to heterozygous data. With the increased interest in haplotype specific analysis, new tools that are designed to be haplotype-aware are necessary that do not have the weaknesses of Quake and ECHO.

Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem

Background

Since the advent of microarray technology, numerous methods have been devised to infer gene regulatory relationships from gene expression data. Many approaches that infer entire regulatory networks. This produces results that are rich in information and yet so complex that they are often of limited usefulness for researchers. One alternative unit of regulatory interactions is a linear path between genes. Linear paths are more comprehensible than networks and still contain important information. Such paths can be extracted from inferred regulatory networks or inferred directly. Since criteria for inferring networks generally differs from criteria for inferring paths, indirect and direct inference of paths may achieve different results.

Results

This paper explores a strategy to infer linear pathways by converting the path inference problem into a shortest-path problem. The edge weights used are the negative log-transformed probabilities of directness derived from the posterior joint distributions of pairwise mutual information between gene expression levels. Directness is inferred using the data processing inequality. The method was designed with two goals. One is to achieve better accuracy in path inference than extraction of paths from inferred networks. The other is to facilitate priorization of interactions for laboratory validation. A method is proposed for achieving this by ranking paths according to the joint probability of directness of each path's edges. The algorithm is evaluated using simulated expression data and is compared to extraction of shortest paths from networks inferred by two alternative methods, ARACNe and a minimum spanning tree algorithm.

Conclusions

Direct path inference appears to achieve accuracy competitive with that obtained by extracting paths from networks inferred by the other methods. Preliminary exploration of the use of joint edge probabilities to rank paths is largely inconclusive. Suggestions for a better framework for such comparisons are discussed.

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data

BACKGROUND

DNA methylation has been linked to many important biological phenomena. Researchers have recently begun to sequence bisulfite treated DNA to determine its pattern of methylation. However, sequencing reads from bisulfite-converted DNA can vary significantly from the reference genome because of incomplete bisulfite conversion, genome variation, sequencing errors, and poor quality bases. Therefore, it is often difficult to align reads to the correct locations in the reference genome. Furthermore, bisulfite sequencing experiments have the additional complexity of having to estimate the DNA methylation levels within the sample.

RESULTS

Here, we present a highly accurate probabilistic algorithm, which is an extension of the Genomic Next-generation Universal MAPper to accommodate bisulfite sequencing data (GNUMAP-bs), that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome. GNUMAP-bs integrates uncertainty from read and mapping qualities to help resolve the difference between poor quality bases and the ambiguity inherent in bisulfite conversion. We tested GNUMAP-bs and other commonly-used bisulfite alignment methods using both simulated and real bisulfite reads and found that GNUMAP-bs and other dynamic programming methods were more accurate than the more heuristic methods.

CONCLUSIONS

The GNUMAP-bs aligner is a highly accurate alignment approach for processing the data from bisulfite sequencing experiments. The GNUMAP-bs algorithm is freely available for download at: http://dna.cs.byu.edu/gnumap. The software runs on multiple threads and multiple processors to increase the alignment speed.

Pathoscope: species identification and strain attribution with unassembled sequencing data

Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner. We present a statistical framework to analyze raw next-generation sequence reads from purified or mixed environmental or targeted infected tissue samples for rapid species identification and strain attribution against a robust database of known biological agents. Our method, Pathoscope, capitalizes on a Bayesian statistical framework that accommodates information on sequence quality, mapping quality, and provides posterior probabilities of matches to a known database of target genomes. Importantly, our approach also incorporates the possibility that multiple species can be present in the sample and considers cases when the sample species/strain is not in the reference database. Furthermore, our approach can accurately discriminate between very closely related strains of the same species with very little coverage of the genome and without the need for multiple alignment steps, extensive homology searches, or genome assembly--which are time-consuming and labor-intensive steps. We demonstrate the utility of our approach on genomic data from purified and in silico "environmental" samples from known bacterial agents impacting human health for accuracy assessment and comparison with other approaches.

Rhizobial plasmids that cause impaired symbiotic nitrogen fixation and enhanced host invasion

The genetic rules that dictate legume-rhizobium compatibility have been investigated for decades, but the causes of incompatibility occurring at late stages of the nodulation process are not well understood. An evaluation of naturally diverse legume (genus Medicago) and rhizobium (genus Sinorhizobium) isolates has revealed numerous instances in which Sinorhizobium strains induce and occupy nodules that are only minimally beneficial to certain Medicago hosts. Using these ineffective strain-host pairs, we identified gain-of-compatibility (GOC) rhizobial variants. We show that GOC variants arise by loss of specific large accessory plasmids, which we call HR plasmids due to their effect on symbiotic host range. Transfer of HR plasmids to a symbiotically effective rhizobium strain can convert it to incompatibility, indicating that HR plasmids can act autonomously in diverse strain backgrounds. We provide evidence that HR plasmids may encode machinery for their horizontal transfer. On hosts in which HR plasmids impair N fixation, the plasmids also enhance competitiveness for nodule occupancy, showing that naturally occurring, transferrable accessory genes can convert beneficial rhizobia to a more exploitative lifestyle. This observation raises important questions about agricultural management, the ecological stability of mutualisms, and the genetic factors that distinguish beneficial symbionts from parasites.

Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.

Parallel Mapping Approaches for GNUMAP

Mapping short next-generation reads to reference genomes is an important element in SNP calling and expression studies. A major limitation to large-scale whole-genome mapping is the large memory requirements for the algorithm and the long run-time necessary for accurate studies. Several parallel implementations have been performed to distribute memory on different processors and to equally share the processing requirements. These approaches are compared with respect to their memory footprint, load balancing, and accuracy. When using MPI with multi-threading, linear speedup can be achieved for up to 256 processors.

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

MOTIVATION

The advent of next-generation sequencing technologies has increased the accuracy and quantity of sequence data, opening the door to greater opportunities in genomic research.

RESULTS

In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable of overcoming two major obstacles in the mapping of reads from next-generation sequencing runs. First, we have created an algorithm that probabilistically maps reads to repeat regions in the genome on a quantitative basis. Second, we have developed a probabilistic Needleman-Wunsch algorithm which utilizes _prb.txt and _int.txt files produced in the Solexa/Illumina pipeline to improve the mapping accuracy for lower quality reads and increase the amount of usable data produced in a given experiment.

AVAILABILITY

The source code for the software can be downloaded from http://dna.cs.byu.edu/gnumap.

Phylogenies scores for exhaustive searches and parsimony scores searches

Fundamental to Multiple Sequence Alignment (MSA) algorithms is modelling insertions and deletions (gaps). The most prevalent model is to use Gap Open Penalties (GOP) and Gap Extension Penalties (GEP). While GOP and GEP are well understood conceptually, their effects on MSA and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the GOP and GEP for three nuclear ribosomal data sets. Particular attention is given to optimal maximum likelihood and parsimony phylogeny scores for various alignments of a range of GOP and GEP and their respective distribution of phylogeny scores.

Pharmacogenomics: analysing SNPs in the CYP2D6 gene using amino acid properties

The CYP2D6 gene is responsible for metabolising a large portion of the commonly prescribed drugs. Because of its importance, various approaches have been taken to analyse CYP2D6 and Single Nucleotide Polymorphisms (SNPs) throughout its sequence. This study introduces a novel method to analyse the effects of SNPs on encoded protein complexes by focusing on the biochemical properties of each non-synonymous substitution using the program TreeSAAP. Our results show four SNPs in CYP2D6 that exhibit radical changes in amino acid properties which may cause a lack of functionality in the CYP2D6 gene and contribute to a person's inability to metabolise specific drugs.

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.

Molecular evidence of field cancerization in a patient with 7 tumors of the aerodigestive tract

Exposure of the mucosa of the upper aerodigestive tract to carcinogens can induce genetic changes resulting in various independent clones of neoplastic growth, a concept defined as "field cancerization." The risk of developing multiple tumors in this compartment of the body is well established. We studied 6 distinct tumors of the upper aerodigestive tract of a single patient for loss of heterozygosity (LOH), microsatellite instability (MSI), p53 mutations, and K-ras codon 12 point mutations. We detected a unique pattern of LOH and p53 mutations in all 6 tumors. No tumor showed a K-ras mutation or MSI. The results support the mechanism of "field cancerization" and illustrate the potential power of molecular techniques to elucidate pathogenesis.

Alterations of the p53 tumor-suppressor gene and K-ras oncogene in perihilar cholangiocarcinomas from a high-incidence area

We observed a clustering of cholangiocarcinoma in a part of West Virginia. We analyzed the frequency and type of alterations in the p53 tumor-suppressor gene and the K-ras oncogene to determine whether cholangiocarcinomas from this high-incidence area differ from other cholangiocarcinomas at the molecular level. We studied 12 carcinomas of patients from the high-incidence area (West Virginia group), and 15 carcinomas of patients from nearby states (non-West Virginia group). Over-expression of the p53 gene product, accompanying most mutations in the p53 gene, was determined by immunohistochemistry. p53 sequence analysis of exons 5, 6, 7, and 8 of the p53-immunohistochemical-positive carcinomas was also performed. K-ras codon 12 mutations were detected by the polymerase chain reaction and allele-specific oligonucleotide hybridization. Significantly more cholangiocarcinomas from the West Virginia group were p53-immunohistochemical-positive than from the non-West Virginia group (67% vs. 20%; p < 0.05). p53 mutations did not differ in the 2 groups in respect to site or specific type. No differences were found between the 2 groups regarding K-ras mutations (17% vs. 27%). Although the higher frequency of p53-immunohistochemical positivity in the West Virginia group may reflect a different etiology of these cholangiocarcinomas, explaining the high incidence in this area, results of p53 sequence analysis were not different in the West Virginia group. The high incidence may be explained by difference in carcinogenic dose or a different etiology not reflected in p53 or K-ras alterations.

Alterations of the p53 tumor-suppressor gene and K-ras oncogene in perihilar cholangiocarcinomas from a high-incidence area

We observed a clustering of cholangiocarcinoma in a part of West Virginia. We analyzed the frequency and type of alterations in the p53 tumor-suppressor gene and the K-ras oncogene to determine whether cholangiocarcinomas from this high-incidence area differ from other cholangiocarcinomas at the molecular level. We studied 12 carcinomas of patients from the high-incidence area (West Virginia group), and 15 carcinomas of patients from nearby states (non-West Virginia group). Over-expression of the p53 gene product, accompanying most mutations in the p53 gene, was determined by immunohistochemistry. p53 sequence analysis of exons 5, 6, 7, and 8 of the p53-immunohistochemical-positive carcinomas was also performed. K-ras codon 12 mutations were detected by the polymerase chain reaction and allele-specific oligonucleotide hybridization. Significantly more cholangiocarcinomas from the West Virginia group were p53-immunohistochemical-positive than from the non-West Virginia group (67% vs. 20%; p < 0.05). p53 mutations did not differ in the 2 groups in respect to site or specific type. No differences were found between the 2 groups regarding K-ras mutations (17% vs. 27%). Although the higher frequency of p53-immunohistochemical positivity in the West Virginia group may reflect a different etiology of these cholangiocarcinomas, explaining the high incidence in this area, results of p53 sequence analysis were not different in the West Virginia group. The high incidence may be explained by difference in carcinogenic dose or a different etiology not reflected in p53 or K-ras alterations.

p53 alterations in atypical alveolar hyperplasia of the human lung

Atypical alveolar hyperplasia (AAH) is a potential precursor lesion from which lung adenocarcinomas arise and may be a good target for studying the early events of lung tumorigenesis. We have previously shown that AAHs are neoplastic epithelial proliferations that often harbor activating mutations of the K-ras oncogene. In the current study, we examined a spectrum of AAHs to determine the frequency and timing of p53 alterations in lung tumorigenesis. We analyzed 37 AAHs and their paired overt lung neoplasms for p53 protein accumulation using the monoclonal antibody DO7. DNA sequence analysis of the p53 gene was performed on those cases demonstrating p53 protein accumulation. AAHs were classified as low-grade, high-grade, or AAH-like carcinoma based on cytoarchitectural features. Accumulation of the p53 protein was found in none (0%) of 20 low-grade AAHs, in 1 (9%) of 11 high-grade AAHs, and in three (50%) of six AAH-like carcinomas. There was a statistically significant trend toward p53 accumulation with increasing grade of the AAHs. A missense mutation in exon 7 of the p53 gene was found in 1 AAH-like carcinoma, whereas mutations in exons 5 through 8 could not be detected in the other three AAHs with p53 protein accumulation. Three of the paired overt carcinomas harbored p53 mutations that were not present in the AAHs. Alterations of p53 do not appear to be common events in AAHs, especially when these lesions exhibit low-grade cytoarchitectural features. Alterations of p53, however, are more frequent at the level of AAH-like carcinoma and may be associated with the transition from a benign to a malignant proliferation of pneumocytes.

Mutational analysis of the P16-binding domain of cyclin-dependent kinase 4 in tumors in the head region of the pancreas

Alterations in genes involved in cell cycle regulation are common in many tumor types. In pancreatic adenocarcinomas, inactivating mutations in the CDKN2 gene, encoding the cyclin-dependent kinase inhibitor p16, are frequently observed. CDKN2 mutations have also been identified in the germline of 50% of patients with hereditary melanoma. Interestingly, such patients also have an increased risk for pancreatic cancers. In melanoma-prone kindreds with CDKN2 wild-type status, a mutation in one of the targets of p16, cyclin-dependent kinase 4 (CDK4) was reported, which abolishes p16 inhibition. To test the possible involvement of CDK4 mutations in pancreatic carcinoma, we analyzed sequence alterations in the p16-binding domain of CDK4 in DNA isolated from 32 tumors in the head region of the pancreas. Alterations in the CDK4 region between codon 1 and codon 56 were not observed in any of the tumors. Our results do not support disruption of the p16 pathway through CDK4 mutation as an oncogenic mechanism in pancreatic head tumorigenesis.

Multiple hyperplastic polyps in the stomach: evidence for clonality and neoplastic potential

The origin and neoplastic potential of gastric epithelial polyps remains an area of great interest, and treatment choices are a topic of controversy. This report describes a patient diagnosed with three concurrent hyperplastic gastric polyps that were studied for genetic alterations. The polyps were investigated for alterations in the K-ras oncogene and the p53 tumor suppressor gene and for p21WAF1/Cip1 and MDM2 protein overexpression. In addition, loss of heterozygosity at several loci that are frequently involved in human cancer was analyzed, microsatellite instability, a hallmark of the "mutator" phenotype, was determined, and Epstein-Barr virus infection was investigated. All separate areas from the three independent polyps harbored the same activating point mutation in codon 12 of the K-ras oncogene, indicating a clonal origin. DNA sequence alterations in p53 were not found, although high p53 protein levels could be shown by immunohistochemistry in areas of carcinoma within the largest polyp. No alterations in any of the other molecular markers were observed. The results strongly favor a clonal origin of the three independent gastric polyps and support the notion that these hyperplastic polyps may carry a risk for malignancy.

Potential false-positive results with antigen enhancement for immunohistochemistry of the p53 gene product in colorectal neoplasms

Immunohistochemistry (IHC) for intranuclear p53 gene product is a simple, routine alternative to molecular genetic analysis of the p53 gene. Several methods for antigen enhancement are currently in use for IHC. This study evaluates the effect of extreme antigen enhancement for p53, using a monoclonal antibody (DO7) and a polyclonal antibody (CM1). The cases studied were five colorectal carcinomas, two specimens of normal colorectal mucosa, and four colorectal carcinomas with genetic alterations which are expected to preclude p53 gene product expression, namely mutation to a STOP codon in the p53 gene detected by denaturing gradient gel electrophoresis with subsequent sequencing and allelic loss of 17p in the region where p53 is located, detected by restriction fragment length polymorphism analysis. The findings suggest that extreme antigen enhancement may cause false-positive results with a distinct nuclear staining pattern when MAb DO7 is used as a primary antibody. It is concluded that all antigen enhancement methods should be thoroughly tested to evaluate their validity and that there may be a limit to the extent to which antigen enhancement can be applied in IHC for p53 protein.

Detection of K-ras mutations in mucinous pancreatic duct hyperplasia from a patient with a family history of pancreatic carcinoma

Mutations in the K-ras oncogene and in the p53 tumor suppressor gene are commonly identified in sporadic cases of pancreatic adenocarcinoma. Although these genes might serve as useful markers for early diagnosis of pancreatic carcinoma in patients at risk for the development of this disease, familial pancreatic carcinomas have not been studied for these mutations. We recently had the opportunity to examine a pancreas prophylactically removed from a patient with a strong family history of pancreatic carcinoma. This gave us the unique opportunity to study the early events in the development of familial adenocarcinoma of the pancreas. Histopathological examination of the pancreas revealed multifocal papillary and nonpapillary mucinous duct hyperplasia. Seven of these foci were microdissected and analyzed for K-ras and p53 mutations. The K-ras mutations were detected by combined mutant-enriched polymerase chain reaction-restriction fragment length polymorphism analysis and characterized further by allele-specific oligonucleotide hybridization. Five of the seven duct lesions harbored activating point mutations in codon 12 of K-ras; a G to A transition was found in four and a G to C transversion in one. In contrast, these lesions did not harbor detectable p53 mutations as determined by denaturing gradient gel electrophoresis of exons 5 to 8, nor was there overexpression of the p53 protein as determined by immunohistochemistry. These findings suggest that mutations in K-ras represent an early event in the pathogenesis of pancreatic carcinoma. In addition, monitoring of patients with a strong family history of pancreatic carcinoma for K-ras mutations may identify patients at risk for the development of invasive carcinoma.

Extrapulmonary pneumocystosis: clinical features in human immunodeficiency virus infection

Pneumocystis carinii infection is reported with increasing frequency as a cause of disease outside of the respiratory tract in patients with human immunodeficiency virus (HIV) infection. Extrapulmonary pneumocystosis is not limited to patients in any discrete risk group for HIV infection. Patients with HIV infection who develop extrapulmonary pneumocystosis frequently do not have concurrent P. carinii pneumonia. Signs and symptoms of extrapulmonary pneumocystosis are nonspecific but when present are frequently referable to the tissues or organs involved. Extrapulmonary pneumocystosis can be diagnosed by examination of tissue biopsies from affected sites using standard histologic techniques. Therapy with antimicrobial agents used to treat P. carinii pneumonia has been effective in some patients. An association between use of aerosolized pentamidine for prevention of P. carinii pneumonia and development of extrapulmonary pneumocystosis has been suggested but remains unconfirmed. Other factors such as the use of zidovudine and duration of immunodeficiency may also be important to the pathogenesis of extrapulmonary pneumocystosis. Further studies are needed to better identify risk factors that may predispose patients to the development of extrapulmonary pneumocystosis.

A survey of adolescents with epilepsy

Thirty-four adolescents with epilepsy, controls matched for age and sex (A) and controls matched for age, sex and general ability (B), were studied. The adolescents with epilepsy were more likely to arrive at school by car or taxi and to have more difficult behaviour in class. Competitive sports were less popular with them and significantly fewer anticipated ever driving a car. Illness and parental marital problems were not a feature of their families. Their comprehension of reading material was significantly poorer than that of control group A. Within the group, the lowest over-all reading scores were found in children with myoclonic seizures, partial seizures with secondary generalisation, or generalised tonic-clonic seizures; and in those whose EEG findings included two-per-second spike and wave, photosensitivity, generalised slow waves, or generalised spike and wave of non-specific frequency. Right focal slow waves, sharp waves and spikes on EEG were associated with problems of comprehension, even when the over-all reading score was acceptable.

Sensitivity of treponemal tests for detecting prior treated syphilis during human immunodeficiency virus infection

To evaluate the sensitivity of treponemal tests as a marker of prior syphilis in individuals with human immunodeficiency virus (HIV) infection, the syphilis serology of 109 homosexual men with a documented history of treated syphilis was compared with records of prior results and confirmed on stored serum samples. None of the HIV-seronegative individuals lost reactivity to a treponemal test, whereas 7% of the seropositive asymptomatic individuals and 38% of those with symptomatic HIV infection had loss of reactivity. Symptomatic HIV infection was associated with loss of reactivity, as a T4 lymphocyte count less than 200 X 10(6)/1, a T4-to-T8 ratio less than 0.6, a single prior episode of syphilis, and a low VDRL titer at the time of the last documented episode of syphilis. Although no conclusions can be drawn about the sensitivity of treponemal tests in patients with active syphilis and HIV infection, these data suggest that treponemal tests may not identify those previously infected with Treponema pallidum.

Sequential serological responses to Aspergillus fumigatus in patients with cystic fibrosis. Use of antigen 'stretching' to delineate IgG and IgE activity

Immunogens from Aspergillus fumigatus were fractionated on the basis of molecular weight. Nine fractions ranging from 900 to 10 kDa were used in ELISA and in a radioallergosorbent test (RAST) with sera from cases of allergic bronchopulmonary aspergillosis (ABPA) and from cystic fibrosis (CF) patients with ABPA or other Aspergillus involvement and compared with control subjects. The profile of IgG reactivity to the nine fractions did not vary substantially for all Aspergillus-involved groups producing peaks at greater than 900 kD and 170 kD whereas the profile for control subjects had a peak at greater than 900 kD only. The IgE profile for CF patients with ABPA did not differ from the profile of the RAST-positive CF patients without ABPA and provided only one peak of activity at 24 kD. Recovery from an episode of ABPA in CF patients was accompanied by a fall in both IgG and IgE antibody levels to all nine fractions, whereas increases in IgG and IgE to all fractions were seen during an episode of ABPA. Although there was an exaggerated IgG increase to antigens in the 43-170 kD range during ABPA, a meaningful increase was also observed to unfractionated A. fumigatus antigen preparations. With IgE in one detailed study the 24-kD fraction provided a better indication of Aspergillus involvement than the unfractionated A. fumigatus antigens. Sequential studies of IgG and IgE levels were not able to predict an episode of ABPA but were useful in conjunction with clinical assessment in following the course of the illness.

Pulmonary diagnostic evaluation in patients suspected of having an HIV-related disease

The wide range of pulmonary infections associated with human immunodeficiency virus (HIV)-seropositivity, coupled with the possible presence of HIV-related neoplasms and non-HIV-related pulmonary processes, requires that most patients who are known to be or suspected of being HIV-seropositive should undergo a thorough diagnostic evaluation. This usually should include a screening evaluation that includes history, physical examination, screening laboratory tests, chest radiography, and arterial blood gas measurements. Pulmonary function testing and lung scanning also may be sensitive in screening, although these and the other procedures are nonspecific. Specific infectious organisms, particularly Pneumocystis carinii, may be identified through examination of induced sputum and by bronchoscopic procedures, including bronchoalveolar lavage and transbronchial biopsy. Open lung biopsy is not a routine part of the diagnostic evaluation. Although detection of recurrent episodes of pneumonia due to P carinii is difficult, empiric diagnosis and treatment of this disorder should be employed primarily when specific diagnostic techniques are unavailable or are refused.

Diagnosis of pulmonary diseases

A broad spectrum of lung disease occurs in association with HIV infection. Included are both infectious and neoplastic processes and idiopathic disorders. To insure prompt, accurate, and efficient diagnosis, a logical, staged sequence of tests should be applied. Chest films and, in some instances, pulmonary function tests and gallium-67 citrate lung scans serve to provide objective indications of lung disease. Each of these tests is sensitive but nonspecific. Specific infecting organisms, particularly P. carinii, can be identified by examining sputum induced by inhalation of 3 per cent saline. Bronchoscopic procedures, including BAL and TBB, are highly sensitive and should be performed in patients having nondiagnostic sputum examinations. Tests involving antigen and antibody detection are of little use in the evaluation of individual patients. Detection of recurrent episodes of PCP is difficult because abnormalities in the usual screening tests may be residual from previous episodes. Finding P. carinii in sputum or bronchoscopic specimens soon (within 2 to 3 months) after a confirmed episode of PCP likely represents residual organisms rather than recrudescence of the infection. Empiric diagnosis of P. carinii should be employed only in limited circumstances when specific diagnostic studies are not available, are contraindicated, or are refused.

Juvenile myoclonic epilepsy

The clinical and electroencephalographic features of 10 adolescents with juvenile myoclonic epilepsy are presented. The mean age on onset was 12.3 years. Myoclonic jerks, predominantly on awakening, occurred in all 10 and were associated with infrequent generalised tonic-clonic seizures in nine. Five had first degree relatives with seizures. The neurodevelopmental status was normal in eight and social integration good in seven. Waking interictal electroencephalograms showed normal background activity in nine, polyspike and wave in six, and single spike and wave in eight. Four were photosensitive. Failure to respond to other antiepileptic drugs was usual, but valproate monotherapy resulted in good or complete seizure control. Juvenile myoclonic epilepsy is a well defined clinical entity that responds well to valproate and is usually associated with a good outlook.