A structured interface to the object-oriented genomics unified schema for XML-formatted data

Data management systems are fast becoming required components in many biology laboratories as the role of computer-based information grows. Although the need for data management systems is on the rise, their inherent complexities can deter the full and routine use of their computational capabilities. The significant undertaking to implement a capable production system can be reduced in part by adapting an established data management system. In such a way, we are leveraging the Genomics Unified Schema (GUS) developed at the Computational Biology and Informatics Laboratory at the University of Pennsylvania as a foundation for managing and analysing DNA sequence data in centromere research projects around Arabidopsis thaliana and related species. Because GUS provides a core schema that includes support for genome sequences, mRNA and its expression, and annotated chromosomes, it is ideal for synthesising a variety of parameters to analyse these repetitive and highly dynamic portions of the genome. Despite this, production-strength data management frameworks are complex, requiring dedicated efforts to adapt and maintain. The work reported in this article addresses one component of such an effort, namely the pivotal task of marshalling data from various sources into GUS. In order to harness GUS for our project, and motivated by efficiency needs, we developed a structured framework for transferring data into GUS from outside sources. This technology is embodied in a GUS object-layer processor, XMLGUS. XMLGUS facilitates incorporating data into GUS by (i) formulating an XML interface that includes relational database key constraint definitions, (ii) regularising traversal through that XML, (iii) realising automatic processing of the XML with database key constraints and (iv) allowing for special processing of input data within the framework for automated processing. The application of XMLGUS to production pipeline processing for a sequencing project and inputting the Arabidopsis genome into GUS is discussed. XMLGUS is available from the Flora website (http://flora.ittc.ku.edu/).

Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars

Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P<0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon- and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the down-regulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

Detecting novel low-abundant transcripts in Drosophila

Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies.

Does measurement instrument moderate the association between the serotonin transporter gene and anxiety-related personality traits? A meta-analysis

We attempted to replicate the findings of two recent meta-analyses that personality inventory moderates the association between the serotonin transporter gene and anxiety-related traits. A total of 24 studies contributed to the meta-analysis, of which three reported genotype frequencies that deviated from Hardy-Weinberg (HW) equilibrium. We found some support for the view that results depend on the type of questionnaire used, although in a direction opposite to that previously reported. Contrasts between the S/S and L/L groups were significant for TCI/TPQ harm avoidance studies (P=0.0024) but not NEO neuroticism (P=0.9757). When studies not in HW equilibrium were excluded the TCI/TPQ result for the S/S genotype still exceeded our 5% threshold, although with reduced significance (P=0.0082), and the NEO result remained nonsignificant (P=0.9109). While we cannot rule out an association between the 5HTT gene and anxiety-related traits, particularly for TCI/TPQ harm avoidance, our findings do indicate that the effect, if present, is small. Our results emphasise the importance of complete ascertainment of studies and the identification of relevant sources of heterogeneity.

Long-term outcome in patients registered with tuberculosis in Zomba, Malawi: mortality at 7 years according to initial HIV status and type of TB

SETTING

Zomba Central Hospital, Malawi.

OBJECTIVES

To determine the outcome of all adult patients who were registered for tuberculosis (TB) treatment 7 years previously according to initial human immunodeficiency virus (HIV) status and type of TB.

DESIGN

A retrospective cohort study of adult patients registered for TB treatment between July and December 1995. Follow-up at patients' homes was performed at the end of treatment, at 32 months and at 84 months (7 years) from the time of TB registration.

FINDINGS

Eight hundred and twenty-seven TB patients were registered: 793 had concordant HIV test results, of whom 612 (77%) were HIV-positive. At 7 years, 136 (17%) patients were alive, 539 (65%) had died and 152 (18%) were lost to follow-up. The death rate for all TB patients was 23.7 per 100 person-years of observation. HIV-positive patients had higher death rates than HIV-negative patients (hazard ratio [HR] 2.2, 95% confidence interval [95%CI] 1.7-2.8). Death rates in smear-negative pulmonary TB patients (HR 2.1, 95%CI 1.7-2.6) and in patients with extra-pulmonary TB (HR 1.7, 95% CI 1.3-2.0) were higher than in patients with smear-positive PTB.

CONCLUSIONS

There was a high mortality rate in TB patients during and after anti-tuberculosis treatment. Adjunctive treatments to reduce death rates are urgently needed.

Motor vehicle driver injury and marital status: a cohort study with prospective and retrospective driver injuries

OBJECTIVE

To investigate the association of marital status with risk of motor vehicle driver injury.

DESIGN

A cohort study with prospective and retrospective outcomes.

SETTING

New Zealand.

PARTICIPANTS

A total of 10,525 adults (a volunteer sample of a multi-industry workforce, n = 8008; and a random sample of urban electoral rolls, n = 2517). EXPOSURE VARIABLE: Self reported marital status, assessed from a questionnaire administered in 1992-93 (baseline).

MAIN OUTCOME MEASURE

Motor vehicle driver injury resulting in admission of the driver to hospital and/or the driver's death, during the period 1988-98; hospitalisation and mortality data were obtained by record linkage to national health databases.

RESULTS

During 108 741 person-years of follow up, 139 driver injury cases occurred (85 before baseline, 54 after). After adjustment for age, sex, and study cohort, never married participants had twice the risk of driver injury (hazard ratio [HR] 2.06, 95% confidence interval [CI] 1.35 to 3.16) as married participants (HR 1.00). The relative risk for never married participants was slightly higher (HR 2.29), though less precise (95% CI 1.39 to 3.76), after further adjustment for alcohol intake, driving exposure, area of residence, body mass index, and occupational status.

CONCLUSIONS

After taking age, sex, and other variables into account, never married people had a substantially higher risk of driver injury than married people. While requiring corroboration, these findings imply that it may be appropriate for driver injury countermeasures to be targeted to never married people.

Pulmonary artery involvement in Wegener's granulomatosis

Classification and nomenclature schemes are guidelines and are not intended to recognize and distinguish the entire spectrum of any single disease. It may in fact be misleading to suggest that a classic presentation of a given disease plus atypical features should be considered an "overlap" of two separate, often rare, conditions. We report a case of typical Wegener's granulomatosis (WG), with the coexistence of pulmonary artery stenosis, a lesion more commonly observed in TA. This is not the first or only example of large vessel vasculitis occurring in patients with WG. This observation cautions clinicians to avoid rigid application of classification and nomenclature systems and raises questions about determinants of vasculitis subsets and organ targeting.

Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries

STUDY OBJECTIVE

To investigate the association between motor vehicle driver injury and socioeconomic status.

DESIGN

Cohort study with prospective and retrospective outcomes.

SETTING

New Zealand.

PARTICIPANTS

10 525 adults (volunteer sample of a multi-industry workforce, n=8008; and a random sample of urban electoral rolls, n=2517).

OUTCOME MEASURE

Motor vehicle driver injury resulting in admission of the driver to hospital or the driver's death, or both, during the period 1988-98; hospitalisation and mortality data were obtained by record linkage to national health databases.

MAIN RESULTS

After adjustment for age and sex, driver injury risk was inversely associated with both occupational status (p for linear trend <0.0001) and educational level (p for linear trend =0.007). Participants in the lowest approximate quartile of occupational status were four times as likely (HR 4.17, 95% CI 2.31 to 7.55) to have experienced a driver injury during follow up as participants in the highest approximate quartile. Participants who had been to secondary school for less than two years were twice as likely (HR 2.26, 95% CI 1.34 to 3.81) to have experienced a driver injury as those who had been to university or polytechnic. There was little evidence that driver injury risk was associated with neighbourhood income (p for linear trend =0.12) CONCLUSIONS: Occupational status and educational level seem to be important determinants of driver injury risk. Driver injury countermeasures should be targeted to people in low status occupations, as well as to people with comparatively little formal education.

Computational Analysis of Gene Identification with SAGE

SAGE is one of the few techniques capable of uniformly probing gene expression at a genome level irrespective of mRNA abundance and without a priori knowledge of the transcripts present. However, individual SAGE tags can match many sequences in the reference database, complicating gene identification. We perform a baseline evaluation of gene identification with SAGE using UniGene Human as the reference database by analyzing 1) the distributions of tags for various length tag sets formed for UniGene Human and 2) the tag-to-sequence mapping using a SAGE tag set consisting of 37,522 tags derived from human myeloid cells. The extensive multiplicity of the dbEST component of UniGene significantly detracts from gains that might be expected by extending tags within the scope of the SAGE protocol. In order to achieve reasonable sequence specificity for gene identification with the content of the commonly used UniGene sequence collection, tags on the order of hundreds of bases in length are required. One way to produce tags of such lengths is with GLGI, which extends SAGE tags to the 3' end of cDNA. We show that the longer sequences produced by GLGI relieve significantly the multiple match condition. In the myeloid sample, we also found a correlation between multiple match severity and high copy number. We extrapolate these findings, providing insights into the use of UniGene Human as a reference for gene identification.

Random errors in the measurement of 10 cardiovascular risk factors

Random errors in the measurement of 10 commonly investigated cardiovascular risk factors (systolic and diastolic blood pressure, blood cholesterol, blood glucose, pulse rate, body mass index (BMI), cigarette consumption, passive smoking, alcohol intake and physical exercise) were assessed in a general population cohort (n = 2517) and a workforce cohort (n = 8008). Random errors were estimated from regression dilution ratios (lower ratios imply greater random error, and a ratio of one implies no random error). All of the risk factors, except for BMI (which had regression dilution ratios of 0.93 and 0.98 in the two cohorts), were measured with substantial levels of random error. Particularly low regression dilution ratios were observed for physical exercise (0.28 and 0.39) and pulse rate (0.47 and 0.56). For each of these risk factors, with the possible exception of BMI, associations with long-term average values could be importantly biased toward the null unless appropriate corrections are made.

Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription

We have analyzed a systematic flaw in the current system of gene identification: the oligo(dT) primer widely used for cDNA synthesis generates a high frequency of truncated cDNAs through internal poly(A) priming. Such truncated cDNAs may contribute to 12% of the expressed sequence tags in the current dbEST database. By using a synthetic transcript and real mRNA templates as models, we characterized the patterns of internal poly(A) priming by oligo(dT) primer. We further demonstrated that the internal poly(A) priming can be effectively diminished by replacing the oligo(dT) primer with a set of anchored oligo(dT) primers for reverse transcription. Our study indicates that cDNAs designed for genomewide gene identification should be synthesized by use of the anchored oligo(dT) primers, rather than the oligo(dT) primers, to diminish the generation of truncated cDNAs caused by internal poly(A) priming.

Correct identification of genes from serial analysis of gene expression tag sequences

SAGE (serial analysis of gene expression) is a remarkable technique for genome-wide analysis of gene expression. It is crucial to understand the extent to which SAGE can accurately indicate a gene or expressed sequence tag (EST) with a single tag. We analyzed the effect of the size of SAGE tag on gene identification. Our observation indicates that SAGE tags are in general not long enough to achieve the degree of uniqueness of identification originally envisaged. Our observations also indicate that the limitation of using SAGE tag to identify a gene can be overcome by converting SAGE tags into longer 3' EST sequences with the generation of longer cDNA fragments from SAGE tages for gene identification (GLGI) method.