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PubMed1996

Development and validation of a Bayesian model for perioperative cardiac risk assessment in a cohort of 1,081 vascular surgical candidates.

OBJECTIVES: This study sought to develop and validate a Bayesian risk prediction model for vascular surgery candidates. BACKGROUND: Patients who require surgical treatment of peripheral vascular disease are at increased risk of perioperative cardiac morbidity and mortality. Existing prediction models tend to underestimate risk in vascular surgery candidates. METHODS: The cohort comprised 1,081 consecutive vascular surgery candidates at five medical centers. Of these, 567 patients from two centers ("training" set) were used to develop the model, and 514 patients from three centers were used to validate it ("validation" set). Risk scores were developed using logistic regression for clinical variables: advanced age (>70 years), angina, history of myocardial infarction, diabetes mellitus, history of congestive heart failure and prior coronary revascularization. A second model was developed from dipyridamole-thallium predictors of myocardial infarction (i.e., fixed and reversible myocardial defects and ST changes). Model performance was assessed by comparing observed event rates with risk estimates and by performing receiver-operating characteristic curve (ROC) analysis. RESULTS: The postoperative cardiac event rate was 8% for both sets. Prognostic accuracy (i.e., ROC area) was 74 +/- 3% (mean +/- SD) for the clinical and 81 +/- 3% for the clinical and dipyridamole-thallium models. Among the validation sets, areas were 74 +/- 9%, 72 +/- 7% and 76 +/- 5% for each center. Observed and estimated rates were comparable for both sets. By the clinical model, the observed rates were 3%, 8% and 18% for patients classified as low, moderate and high risk by clinical factors (p<0.0001). The addition of dipyridamole-thallium data reclassified >80% of the moderate risk patients into low (3%) and high (19%) risk categories (p<0.0001) but provided no stratification for patients classified as low or high risk according to the clinical model. CONCLUSIONS: Simple clinical markers, weighted according to prognostic impact, will reliably stratify risk in vascular surgery candidates referred for dipyridamole-thallium testing, thus obviating the need for the more expensive testing. Our prediction model retains its prognostic accuracy when applied to the validation sets and can reliably estimate risk in this group.

Aged↗

PubMed1989

Responsiveness and validity in health status measurement: a clarification.

We present data from two studies which clarify the relationship between the responsiveness and validity of instruments designed to measure health status in clinical trials. In a controlled trial of long vs short duration adjuvant chemotherapy for women with Stage II breast cancer, the Breast Cancer Chemotherapy Questionnaire (BCQ) proved valid as a measure of subjective health status and was able to distinguish long vs short arms. Well validated measures of physical and emotional function developed by the Rand Corporation were unable to distinguish between the two groups. The Eastern Co-operative Oncology Group Criteria (ECOG) distinguished the two groups, but failed criteria of clinical sensibility as a measure of subjective health status. In a study of patients with Crohn's disease and ulcerative colitis, the Inflammatory Bowel Disease Questionnaire (IBDQ) showed small intrasubject variability over time. Gobal ratings of change showed moderate to high correlations with changes in IBDQ score, and patients who reported overall improvement or deterioration showed large changes in IBDQ score. Each of these findings support, in different ways, the reproducibility, validity, and responsiveness of the questionnaire. While the same data can at times bear on both validity and responsiveness, when assessing evaluative instruments it is useful to make a conceptual distinction between the two.

Breast Neoplasms↗

PubMedDate not supplied

Validation of defining characteristics of four nursing diagnoses using a computerized data base.

As the use of nursing diagnoses in clinical practice increases, systematic research is necessary to appropriately validate them. Validity studies could be expedited by the use of information technology and computerized clinical data bases. The purpose of the following descriptive study was to validate the defining characteristics (risk factors for potential diagnoses) of the four nursing diagnoses related to alterations in fluid volume proposed by the North American Nursing Diagnosis Association using a nursing minimum data set (NMDS) collected from a computerized nursing data base. A sensitivity measure, the proportion of subjects with specific defining characteristics for a given diagnosis among the total number of subjects with the respective diagnosis, was used to estimate validity. The study was conducted in a 265-bed, mid-western, community hospital in which computerized nursing diagnosis care planning is used. The elements of the NMDS and defining characteristics were collected from a systematic sample (N = 191). The sample consisted of a proportion of about half of computerized discharge patient care plan summaries from each of the four diagnostic labels related to alteration in fluid volume obtained from medical records during the 1987 calendar year. Discharge patient care plan summaries contained at least one of four nursing diagnoses related to alteration in fluid volume. The results show the existence of individual defining characteristics as well as combinations of defining characteristics meeting validation criteria for each diagnostic label. Never-documented defining characteristics also were identified.

Adolescent↗

PubMed2005

The reliability and validity of assessment of sagittal plane deviations in children who have spastic diplegia.

OBJECTIVE: To assess the reliability and validity of a newly described classification of sagittal plane alignment in spastic diplegic gait. DESIGN: Twenty split-screen videos of children with spastic diplegia, Gross Motor Function Classification System levels I to III, were viewed on 2 occasions, 6 weeks apart, by 5 raters. The sagittal plane alignments of the right and left lower limbs in gait were classified separately as true equinus, jump knee, apparent equinus, or crouch, based on the published classification. A fifth category, nonclassifiable, was used if classification was not possible. We then used sagittal plane kinematic data to confirm the classification for each subject and these were compared with rater classification scores, which used the video information only. SETTING: Tertiary-level children's hospital. PARTICIPANTS: Three pediatric orthopedic surgeons and 2 pediatric orthopedic residents. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Gait classification scores derived from visual observation were compared among and within raters. The gait classification scores derived from visual observation were compared with the scores derived from sagittal plane kinematic data to assess validity. RESULTS: A moderate correlation was found among the 5 raters within each session, with an interrater weighted kappa score of .45 in session 1 and .49 in session 2. The intrarater, weighted kappa scores showed a moderate to substantial level of agreement between sessions, ranging from .50 to .68. The classification scores of individual raters had moderate validity when compared with classifications derived from the sagittal plane kinematic data. However, there was a substantial level of agreement between the consensus opinion and the classification obtained using the kinematic data as well as the video recordings (weighted kappa=0.8). CONCLUSIONS: This classification has only moderate reliability and validity when a single experienced rater views the 2-dimensional gait videos. However, the consensus opinion derived from the scores of 5 raters considerably improves the validity of the assessment.

Biomechanical Phenomena↗

PubMed2006

A systematic investigation of the rate laws valid in intracellular environments.

Recently there has been significant interest in deducing the form of the rate laws for chemical reactions occurring in the intracellular environment. This environment is typically characterized by low-dimensionality and a high macromolecular content; this leads to a spatial heterogeneity not typical of the well stirred in vitro environments. For this reason, the classical law of mass action has been presumed to be invalid for modeling intracellular reactions. Using lattice-gas automata models, it has recently been postulated [H. Berry, Monte Carlo simulations of enzyme reactions in two dimensions: Fractal kinetics and spatial segregation, Biophys. J. 83 (2002) 1891-1901; S. Schnell, T.E. Turner, Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws, Prog. Biophys. Mol. Biol. 85 (2004) 235-260] that the reaction kinetics is fractal-like. In this article we systematically investigate for the first time how the rate laws describing intracellular reactions vary as a function of: the geometry and size of the intracellular surface on which the reactions occur, the mobility of the macromolecules responsible for the crowding effects, the initial reactant concentrations and the probability of reaction between two reactant molecules. We also compare the rate laws valid in heterogeneous environments in which there is an underlying spatial lattice, for example crystalline alloys, with the rate laws valid in heterogeneous environments where there is no such natural lattice, for example in intracellular environments. Our simulations indicate that: (i) in intracellular environments both fractal kinetics and mass action can be valid, the major determinant being the probability of reaction, (ii) the geometry and size of the intracellular surface on which reactions are occurring does not significantly affect the rate law, (iii) there are considerable differences between the rate laws valid in heterogeneous non-living structures such as crystals and those valid in intracellular environments. Deviations from mass action are less pronounced in intracellular environments than in a crystalline material of similar heterogeneity.

Fractals↗

PubMed2005

Assessing the validity and responsiveness of disease-specific quality of life instruments in intermittent claudication.

PURPOSE: To recommend a suitable disease-specific quality of life (QOL) instrument for use in intermittent claudication (IC) based on validity and responsiveness. METHODS: Seventy claudicants completed two generic (SF36 and EUROQOL) and three disease-specific (CLAUS, VASCUQOL and SIP(IC)) QOL instruments prior to and 6 months after treatment (angioplasty or conservative therapy). Ankle brachial pressure indices and treadmill walking distances were measured at each assessment and International Society of Cardiovascular Surgery (ISCVS) recommended outcome measures were used to stratify the results. Construct and convergent-divergent validity was assessed for the three disease-specific QOL instruments. Responsiveness was assessed using effect sizes (effect size >0.5 is clinically significant). RESULTS: All clinical indicators improved significantly following treatment. All five domains of CLAUS, the VASCUQOL and SIP(IC) showed highly significant spearman correlation with intermittent claudication distance (ICD) and maximum walking distance (MWD) (0.267-0.697, p=0.01), suggesting good construct validity. There was greater correlation between like domains of CLAUS and SF36 than non-like domains suggesting good convergent-divergent validity. Pain domain of CLAUS and VASCUQOL could detect mild clinical improvement significantly (effect sizes 0.55 and 0.67). Pain and everyday life domain of CLAUS and the VASCUQOL could detect moderate clinical improvement significantly (effect sizes 0.7, 0.74 and 0.56, respectively). CONCLUSION: The three disease-specific QOL instruments (CLAUS, VASCUQOL, SIP(IC)) showed a high degree of construct and convergent-divergent validity. Amongst the three disease-specific QOL instruments, the VASCUQOL was most responsive and we would recommend its use in clinical practice.

Aged↗

PubMed2006

A novel method of producing a repetitive dynamic signal to examine reliability and validity of gait analysis systems.

Gait dysfunction is a common functional complaint of clients who seek medical care. Gait dysfunction can be caused by musculoskeletal disorders such as osteoarthritis or fractures, or it can be caused by neuromuscular disorders such as multiple sclerosis or cerebrovascular accident. Decisions made by health care providers working with these clients could be enhanced by the availability of valid and reliable gait measurement. Valid and reliable gait measurement is possible with laboratory-based motion analysis systems, but these are not universally available. Several portable systems collect footfall data and provide a relatively inexpensive alternative to sophisticated motion analysis systems. However, data collected by these portable systems cannot be used with confidence because of the lack of verification of the validity and reliability of the data they collect about movement. This paper describes a novel method of examining test-retest reliability and concurrent validity that produces a signal with minimal variation. To produce repetitive distance and timing events, a cylindrical weight was rolled across the field of both the laboratory motion analysis system and the system to be evaluated. Measures of the weight's movement were taken simultaneously with both systems. A reference point was chosen to allow for comparison between the systems. The spatial measure that was compared between systems was the horizontal distance between successive repetitions of the reference point's vertical position. The temporal measure that was compared between systems was the time between successive repetitions of the reference point's vertical position. The method described in this paper provides a minimally variable repetitive signal that can be used to investigate concurrent validity of gait analysis systems.

Biomechanical Phenomena↗

PubMed2006

Reliability and predictive validity of the Asthma Control Test administered by telephone calls using speech recognition technology.

BACKGROUND: The Asthma Control Test (ACT) has been validated in a paper and pencil version but has not been validated for use by telephone. OBJECTIVE: The purpose of this study was to provide validation data for the ACT administered by interactive telephone calls using speech recognition technology. METHODS: The ACT was administered to patients who confirmed a diagnosis of physician-diagnosed asthma, and information regarding race/ethnicity, smoking, and asthma course was also obtained during the call. Asthma emergency department visits, hospitalizations, and oral corticosteroid and beta-agonist canister dispensings were assessed for the 12 months after the date of each patient's call. Internal consistency reliability and predictive validity were assessed. RESULTS: Asthma Control Test scores (higher indicates better control) were completed by 2244 patients and were inversely related to black or Hispanic race/ethnicity and smoking. Reliability was 0.83. ACT scores were significantly related to emergency hospital care and oral corticosteroid and beta-agonist dispensings over the period of the subsequent 6 and 12 months. After adjusting for demographic characteristics, a score < or = 15 was associated significantly with an increased 12-month risk of emergency hospital care (odds ratio [OR], 2.5), oral corticosteroid dispensings (OR, 2.6) and dispensing of more than 6 beta-agonist canisters (OR, 6.8) compared with a score > or = 20. CONCLUSION: These data support the reliability and predictive validity of the ACT administered by interactive telephone calls using speech recognition technology. CLINICAL IMPLICATIONS: The ACT can be used for outreach or follow-up by means of interactive telephone calls using speech recognition technology.

Adrenal Cortex Hormones↗

PubMed2005

Reliability and validity of the PORPUS, a combined psychometric and utility-based quality-of-life instrument for prostate cancer.

BACKGROUND: Although utility-based quality-of-life instruments are often used in economic evaluations and psychometric instruments in treatment evaluations, these are complementary approaches to assessing outcomes. In this study we developed and tested these two forms of quality-of-life instruments, both based on a single, validated, health classification system. OBJECTIVES: To assess the measurement properties (reliability and validity) of two newly developed psychometric and utility-based instruments for assessing outcomes associated with prostate cancer. METHODS: 141 men with cancer of the prostate (CaP), treated with radical prostatectomy, radiation therapy, hormonal therapy, and/or chemotherapy were assessed with both instruments and other standard psychometric and utility-based instruments. RESULTS: Analyses indicate the test instruments are reliable and valid. Full-scale correlations between the instruments and standard instruments indicate validity, as do correlations of key subscales, and an evaluation of linear associations with the UCLA-Prostate Cancer Symptom Scales. CONCLUSION: Evidence from this study supports the reliability and construct validity of the tested instruments. Prostate cancer outcomes can now be assessed by a combination of psychometric and utility-based methods, allowing a ready comparison of derived outcomes.

Aged↗

PubMed2006

Statistical external validation and consensus modeling: a QSPR case study for Koc prediction.

The soil sorption partition coefficient (log K(oc)) of a heterogeneous set of 643 organic non-ionic compounds, with a range of more than 6 log units, is predicted by a statistically validated QSAR modeling approach. The applied multiple linear regression (ordinary least squares, OLS) is based on a variety of theoretical molecular descriptors selected by the genetic algorithms-variable subset selection (GA-VSS) procedure. The models were validated for predictivity by different internal and external validation approaches. For external validation we applied self organizing maps (SOM) to split the original data set: the best four-dimensional model, developed on a reduced training set of 93 chemicals, has a predictivity of 78% when applied on 550 validation chemicals (prediction set). The selected molecular descriptors, which could be interpreted through their mechanistic meaning, were compared with the more common physico-chemical descriptors log K(ow) and log S(w). The chemical applicability domain of each model was verified by the leverage approach in order to propose only reliable data. The best predicted data were obtained by consensus modeling from 10 different models in the genetic algorithm model population.

Algorithms↗

PubMed2006

Cross-cultural adaptation and validation of Singapore English and Chinese versions of the Lequesne Algofunctional Index of knee in Asians with knee osteoarthritis in Singapore.

OBJECTIVE: To cross-culturally adapt and validate Singapore English and Chinese versions of the Lequesne Algofunctional Index of knee in patients with knee osteoarthritis (OA) in Singapore. METHODS: Singapore English and Chinese versions were cross-culturally adapted from the source English version following standard guideline (including cognitive debriefing). Patients were asked to complete an identical, pretested questionnaire containing the Lequesne index, Short Form 36 Health Survey (SF-36), and EQ-5D twice within 6 days. Reliability was assessed using Cronbach's alpha and intraclass correlation coefficients (ICC). Dimensionality was assessed by principal component factor analysis. Construct validity was tested by item-to-scale correlations and 12 and six a priori hypotheses for convergent and divergent construct validities, respectively. RESULTS: Singapore English and Chinese Lequesne indices were well accepted by patients in pilot testing and were therefore administered to a consecutive sample of 127 English- and 131 Chinese-speaking Singaporeans with knee OA. Acceptable internal consistency was observed for activities of daily living and the global index (alpha=0.72-0.82), and the good test-retest reliability for all scales in both versions (ICC=0.66-0.94). Expected item-to-scale correlations were presented only in activities of daily living in both versions. Factor analysis yielded two factors for both versions. Convergent and divergent construct validities were supported by the presence of hypothesized correlations between the Lequesne index and SF-36 and EQ-5D scales. CONCLUSION: Both versions of the Lequesne index demonstrated acceptable reliability and validity among multiethnic Asian patients with knee OA, which suggests that it could be used as a global index in the health-related quality of life (HRQoL) measurements in Singapore and possibly other Asian countries.

Activities of Daily Living↗

PubMed2006

Validity of self-report measures of pain and disability for persons who have undergone arthroplasty for osteoarthritis of the carpometacarpal joint of the hand.

OBJECTIVE: To establish the validity of three self-report scales used to measure function following arthroplasty for osteoarthritis (OA) of the carpometacarpal joint. METHOD: Persons with OA of the carpometacarpal joint (n=122) were assessed on one occasion 9-117 months following tendon interposition arthroplasty. They completed three self-report measures of hand/upper limb disability: the Australian/Canadian Osteoarthritis Hand Index (AUSCAN), the Patient-Rated Wrist Hand Evaluation (PRWHE), and the Disabilities of Arm, Shoulder and Hand (DASH). They also completed the Short Form 36 (SF-36) and performed tests of strength, range of motion (ROM), and dexterity. Factor analysis and correlations were used to determine the association among the scales and subscales considered to measure similar constructs (e.g., pain and physical disability). Correlations between the scales and measures of impairment were also conducted to examine construct validity of the disability measures. t-Tests evaluated the hypotheses that subjects with isolated hand OA would have lower scores than those with additional joint involvement. RESULTS: All three scales or their subscales loaded on one factor. Convergent validity of the disability measures was demonstrated by high correlations between similar subscales (r>0.75), and divergent validity by a lack of correlation between the measures and self-report hand appearance. As expected, correlations between disability and strength, dexterity, or a global measure of ROM were higher than with ROM of individual joints. The AUSCAN and the DASH were better able to discriminate those with localized hand OA from those with involvement of other joints. CONCLUSIONS: The AUSCAN, PRWHE, and DASH are valid assessments of pain and/or disability of hand OA, and provide information distinct from impairment measures.

Activities of Daily Living↗

PubMed2005

Cancer-related symptom assessment in Russia: validation and utility of the Russian M. D. Anderson Symptom Inventory.

This multicenter cross-sectional study (n=226) validated the Russian-language M. D. Anderson Symptom Inventory (MDASI-R) in Russian cancer patients with hematological malignancies or solid tumors. The Russian-language Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36-R) also was used for validation. Factor analysis found three underlying constructs for symptom items--general, treatment-related, and affective symptoms--with Cronbach alphas of 0.86, 0.68, and 0.90, respectively. Convergent validity was established by comparing MDASI-R items with SF-36-R subscales. The MDASI-R detected significant differences in symptom severity and interference levels by performance status, supporting known-group validity. The most prevalent symptoms were fatigue, sleep disturbance, pain, sadness, and poor appetite; 53% of the sample reported one to four moderate-to-severe symptoms (>or=5 on 0-10 scale). Symptoms interfered most with work and general activity. Medical professionals underestimated the severity of pain, fatigue, and distress. The MDASI-R is valid and reliable for measuring symptom severity and interference in Russian cancer patients.

Adolescent↗

PubMed2006

Cleaning verification assays for highly potent compounds by high performance liquid chromatography mass spectrometry: strategy, validation, and long-term performance.

A cleaning-verification assay was validated for a highly potent family of compounds utilizing a swab-sampling procedure and high performance liquid chromatography mass spectrometry (LC-MS) for separation and detection of the analytes. Due to the high potency of the compound, the LC-MS method was validated at a level of 50 ng/25 cm(2) and 50 ng/100 cm(2) (which equates to 10 ng/ml after extraction in 5 ml of sample solvent, and 3 ng/ml after correction for sampling losses). This validation exercise included recovery estimates from all drug product contact surfaces within the clinical trial manufacturing equipment, namely, stainless steel, anodized aluminum, Rilsan coated aluminum, bronze, polyvinylchloride, and Oilon. The limit of detection for the LC-MS method was determined to be less than 0.5 ng/ml, or less than 0.1 ng/cm(2), of the analyte. This method does not employ an internal standard. Long-term performance of the validated method is also reported. The precision on replicate injections of the standard prepared in the range of 3-6 ng/ml was typically better than 8.0% relative standard deviation (R.S.D.) over the course of 1 year, which resulted from 10 cleaning-verification submissions. Those results were consistent with the data obtained during method validation.

Acetates↗

PubMed2006

A novel quantitative cross-validation of different cortical surface reconstruction algorithms using MRI phantom.

Cortical surface reconstruction is important for functional brain mapping and morphometric analysis of the brain cortex. Several methods have been developed for the faithful reconstruction of surface models which represent the true cortical surface in both geometry and topology. However, there has been no explicit comparison study among those methods because each method has its own procedures, file formats, coordinate systems, and use of the reconstructed surface. There has also been no explicit evaluation method except visual inspection to validate the whole-cortical surface models quantitatively. In this study, we presented a novel phantom-based validation method of the cortical surface reconstruction algorithm and quantitatively cross-validated the three most prominent cortical surface reconstruction algorithms which are used in Freesurfer, BrainVISA, and CLASP, respectively. The validation included geometrical accuracy and mesh characteristics such as Euler number, fractal dimension (FD), total surface area, and local density of points. CLASP showed the best geometric/topologic accuracy and mesh characteristics such as FD and total surface area compared to Freesurfer and BrainVISA. In the validation of local density of points, Freesurfer and BrainVISA showed more even distribution of points on the cortical surface compared to CLASP.

Algorithms↗

PubMed2004

Validity and reliability of the PDQ-39 and the PDQ-8 in English-speaking Parkinson's disease patients in Singapore.

The purpose of the study was to assess the validity and reliability of the Parkinson's disease questionnaire (PDQ-39, UK English version) as well as its briefer version (the PDQ-8) among Asian patients with Parkinson's disease (PD) in Singapore. Eighty-eight patients recruited from movement disorder clinics or patient support groups completed the PDQ-39 and EQ-5D, a generic health related quality of life questionnaire previously validated for use in Singapore. PDQ-39 items showed good convergent and discriminant validity. Construct validation against the EQ-5D showed strong correlation between these scales as hypothesised (Spearman's rho: 0.53-0.71, P<0.001 for all). Factor analysis yielded a component on which all eight PDQ-39 dimensions were substantially loaded (loading range: 0.50-0.79). The PDQ-39 also demonstrated acceptable internal consistency (Cronbach's alpha: 0.59-0.94) and test-retest reliability (intra-class correlation coefficient:0.67-0.87, n=68). Six of eight PDQ-8 items showed the strongest correlation with their PDQ-39 dimensions as hypothesised. PDQ-39 and PDQ-8 summary indexes were highly correlated (Pearson's r=0.96, ICC=0.95), and both were strongly correlated with the EQ-5D utility index and EQ-5D visual analogue scale (P<0.001). We conclude that the PDQ-39 and PDQ-8 are valid and reliable disease-specific HRQoL instruments for PD in Singapore.

Adult↗

PubMedDate not supplied

An assessment tool for brachial plexus regional anesthesia performance: establishing construct validity and reliability.

BACKGROUND AND OBJECTIVES: Technical proficiency in regional anesthesia is often determined subjectively through in-training evaluations. Objective assessment tools improve these evaluations by providing criteria for measurement. However, any evaluation instrument needs to be valid and reliable before it is adopted into a curriculum. The purpose of this study is to determine the validity and reliability of a devised assessment of residents performing an interscalene brachial plexus block (ISB). METHODS: In this prospective study, 10 junior trainees and 10 senior trainees were videotaped performing an ISB. Junior trainees were defined as in their first year of anesthetic training and had performed less than 10 ISBs independently. Senior trainees had completed at least 1 year of anesthesia training and had performed greater than 10 ISBs independently. Two blinded expert raters independently evaluated the performance of the ISB using a checklist and global rating scale. Construct validity was established if the assessments were able to reliably discriminate between different levels of training. RESULTS: Senior trainees performed an ISB significantly better than junior trainees when assessed using the global rating scale (P < .05) and checklist (P < .001). The overall interrater reliability for the global rating scores was excellent (r = 0.85, P < .05) and was good for the checklist scores (r = 0.74, P < .05). CONCLUSIONS: Both assessment modalities were valid, in that they reliably discriminated between different levels of training. Objective measures of technical skills are feasible, timely, and improve the validity and reliability of competency assessments.

Anesthesia, Conduction↗

PubMed2006

An efficient and high-throughput approach for experimental validation of novel human gene predictions.

A highly automated RT-PCR-based approach has been established to validate novel human gene predictions with no prior experimental evidence of mRNA splicing (ab initio predictions). Ab initio gene predictions were selected for high-throughput validation using predicted protein classification, sequence similarity to other genomes, colocalization with an MPSS tag, or microarray expression. Initial microarray prioritization followed by RT-PCR validation was the most efficient combination, resulting in approximately 35% of the ab initio predictions being validated by RT-PCR. Of the 7252 novel genes that were prioritized and processed, 796 constituted real transcripts. In addition, high-throughput RACE successfully extended the 5' and/or 3' ends of >60% of RT-PCR-validated genes. Reevaluation of these transcripts produced 574 novel transcripts using RefSeq as a reference. RT-PCR sequencing in combination with RACE on ab initio gene predictions could be used to define the transcriptome across all species.

Algorithms↗