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Positioning a medical school for modern biomedical research: the department of genome sciences at the University of Washington School of Medicine.

The availability of genome sequences from a multitude of organisms, which began about a decade ago, has had enormous impact throughout the biomedical sciences. These sequence data have changed the way research studies are carried out and have led to the explosive growth of computational biology as an approach to analyze biological processes and evolution. In medicine, the completion of the human genome sequence has illuminated the function of many genes, facilitated the correlation of mutant genes to disease phenotypes, and provided a basis for the study of human variation. At the University of Washington, the two academic departments whose overall programs were most centrally affected by the sequencing revolution were Genetics and Molecular Biotechnology. These departments were fused in 2001 to form the Department of Genome Sciences in order to best exploit these developments and to become a prototype for the basic biomedical science department of the future. The department's goal is to address leading-edge questions in biology and medicine through the application of genetics, genomics, proteomics, and computational approaches to the increasing collection of known genome sequences and their encoded products. The authors review the events that led up to the founding of this department and discuss the initiatives that have been undertaken, which include the recruitment of faculty, the establishment of a new interdisciplinary graduate program, the continued development of an outreach program, and the construction of a building to house the department. Lessons learned in crafting this department are also discussed, as well as how these might apply to other medical schools.

Biomedical Research↗

Somatic cell count distributions during lactation predict clinical mastitis.

This research investigated somatic cell count (SCC) records during lactation, with the purpose of identifying distribution characteristics (mean and measures of variation) that were most closely associated with clinical mastitis. Three separate data sets were used, one containing quarter SCC (n = 1444) and two containing cow SCC (n = 933 and 11,825). Clinical mastitis was defined as a binary outcome, present or absent, for each lactation, and SCC were log (base 10) transformed. A generalized linear mixed model within a Bayesian framework was used for analysis. Parameters were estimated using Markov Chain Monte Carlo with Gibbs sampling. Results from the 3 data sets were similar. Increased maximum and standard deviation log SCC during lactation, rather than increased geometric mean, were the best overall indicators of clinical mastitis. Distributions of SCC were also investigated separately for different mastitis pathogens. Increased maximum log SCC was associated with clinical mastitis caused by all pathogen types. Increased standard deviation log SCC was associated with Staphylococcus aureus, and Streptococcus uberis clinical mastitis and increased coefficient of variation log SCC (standard deviation divided by mean) was associated with Escherichia coli clinical mastitis. Increased geometric mean lactation SCC was associated with an increased risk of Staph. aureus clinical mastitis but a reduced risk of E. coli clinical mastitis. Our results suggest that using measures of variation and maximum cow SCC would enhance the accuracy of predicting clinical mastitis, compared with geometric mean SCC, and therefore improve genetic programs that aim to select for clinical mastitis resistance. The results are also consistent with low SCC increasing susceptibility to some mastitis pathogens.

Animals↗

[Differentiation, identification and development of database of T. aestivum L. varieties of Ukrainian selection on the basis of sequence-tagged analysis of microsatellite repeats].

Determination of the variety genotype is very important for the development of theory and practice of plant breeding and for right protection of a variety originator. In this reason attention is focused on the molecular markers generated by polymerase chain reaction. On the basis of STMS-analysis principles of identification and development of database, which reflect molecular-genetics peculiarities of some varieties of the Plant Breeding and Genetics Institute and other Ukrainian breeding organizations, are formulated. Allelic state at microsatellite loci and their distribution were investigated. Wheat varieties were ranged according to genetic distances, data on pedigree and cluster distribution of varieties obtained using computer programs were compared.

Cluster Analysis↗

Genetic heterogeneity within electrophoretic "alleles" of xanthine dehydrogenase in Drosophila pseudoobscura.

An experimental plan for an exhaustive determination of genic variation at structural gene loci is presented. In the initial steps of this program, 146 isochromosomal lines from 12 geographic populations of D. pseudoobscura were examined for allelic variation of xanthine dehydrogenase by the serial use of 4 different electrophoretic conditions and a head stability test. The 5 criteria revealed a total of 37 allelic classes out of the 146 genomes examined where only 6 had been previously revealed by the usual method of gel electrophoresis. This immense increase in genic variation also showed previously unsuspected population differences between the main part of the species distribution and the isolated population of Bogotá population. The average heterozygosity at the Xdh locus is at least 72% in natural populations. This result, together with the very large number of alleles segregating and the pattern of allelic frequencies, has implications for theories of genetic polymorphism which are discussed.

Alleles↗

Design of long oligonucleotide probes for functional gene detection in a microbial community.

MOTIVATION: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes. RESULTS: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set. AVAILABILITY: http://brcapp.kribb.re.kr/HPD/

Algorithms↗

Association between genetic variation in the gene for death-associated protein-3 (DAP3) and adult asthma.

Lung epithelium plays a central role in modulation of the lung inflammatory response, and lung repair and airway epithelial cells are targets in asthma and viral infection. Activated T lymphocytes release cytokines such as interferon-gamma (IFN-gamma) that induce apoptosis, or programmed cell death, of damaged epithelial cells. Death-associated protein-3 (DAP3) is involved in mediating IFN-gamma-induced cell death. To assess the possible involvement of genetic variants of DAP3 with asthma, we searched for single-nucleotide polymorphisms (SNPs) in the gene and conducted a case-control study with 1,341 subjects. We found a strong association between bronchial asthma (BA) in adults (P=0.0051, odds ratio=1.87, 95% CI=1.20-2.92), whereas no association was found with childhood asthma. The tendency was more prominent in patients with higher serum total immunoglobulin E (IgE) (>250 IU/ml) (P=0.00061, odds ratio=2.40, 95% CI=1.44-4.00). DAP3 was expressed in normal bronchial epithelial cells, and the expression was induced by IFN-gamma. These results indicated that specific variants of the DAP3 gene might be associated with the mechanisms responsible for adult BA and contribute to airway inflammation and remodeling.

Adolescent↗

Random amplified polymorphic DNA (RAPD) analysis in Indian mung bean (Vigna radiata (L.) Wilczek) cultivars.

Greengram [Vigna radiata (L.) Wilczek], also known as mung bean, widely cultivated in a large number of countries, is an important pulse crop of Asia and is considered one of the ancestral species of the genus Vigna. Since yields of greengram have remained low across subtropical and tropical Asia, it is important to estimate genetic diversity in existing cultivars in order to see if the lack of genetic variability might be a constraining factor. In this study, 32 Indian cultivars of greengram were subjected to random amplified polymorphic DNA (RAPD) analysis using 21 decamer primers. A total of 267 amplification products were formed at an average of 12.71 per primer with an overall polymorphism of 64%. The extent of polymorphism was moderate to low. Jaccard similarity coefficient values ranged from 0.65 to 0.92. The cluster analysis resulted in mainly three clusters revealing greater homology between cultivars released from the same source. The results of principal components analysis also substantiated this conclusion. The close genetic similarity between the cultivars could be explained due to the high degree of commonness in their pedigrees. The narrow genetic base of the greengram cultivars revealed in the present analysis emphasises the need to exploit the large germplasm collections having diverse morphoagronomic traits in cultivar improvement programs.

Crops, Agricultural↗

Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend.

The recommendation of new plant varieties for commercial use requires reliable and accurate predictions of the average yield of each variety across a range of target environments and knowledge of important interactions with the environment. This information is obtained from series of plant variety trials, also known as multi-environment trials (MET). Cullis, Gogel, Verbyla, and Thompson (1998) presented a spatial mixed model approach for the analysis of MET data. In this paper we extend the analysis to include multiplicative models for the variety effects in each environment. The multiplicative model corresponds to that used in the multivariate technique of factor analysis. It allows a separate genetic variance for each environment and provides a parsimonious and interpretable model for the genetic covariances between environments. The model can be regarded as a random effects analogue of AMMI (additive main effects and multiplicative interactions). We illustrate the method using a large set of MET data from a South Australian barley breeding program.

Analysis of Variance↗

[The polymorphism of the kappa-casein gene and its connection to economically valuable traits in cattle].

The literature data on milk protein (particularly kappa-casein) polymorphism study in different cattle breeds are represented. Allele variants of kappa-kasein are associated with lactation and have an influence on the composition of milk and its properties, including cheese-making properties. The importance of ways of kappa-casein genetic variants use in concrete selection programs are discussed.

Alleles↗

Wide variation in microsatellite sequences within each Pfcrt mutant haplotype.

Flanking microsatellites for each of the Pfcrt mutant haplotype of Plasmodium falciparum remain conserved among geographical isolates. We describe here heterogeneity in the intragenic microsatellites among each of the Pfcrt haplotype. There were fourteen different alleles of AT repeats of intron 2 and eight alleles of TA repeats of intron 4 of the pfcrt gene among Indian isolates. This resulted in 33 different two-locus (intron 2 plus intron 4) microsatellite genotypes among 224 isolates. There were 15 different two-locus microsatellite genotypes within the South American Pfcrt haplotype (S72V73M74N75T76S220) and 11 genotypes in the southeast Asian haplotype (C72V73I74E75T76S220) in these isolates. Indian isolates with Pfcrt haplotype C72V73I74E75T76S220 shared one of its two-locus microsatellite genotype with southeast Asian P. falciparum parasite lines from Thailand (K1) and Indochina (Dd2 and W2). Conversely, Indian isolates containing S72V73M74N75T76S220 Pfcrt haplotype did not share any of their two-locus microsatellite genotype with South American parasite line 7G8 from Brazil. Significantly, large number of newer two-locus microsatellite genotypes were detected in a 2-year time period (P<0.05). Microsatellite variation was more prominent in the areas of high malaria transmission. It is concluded that the genetic recombination in the intragenic microsatellites continues in the parasite population even after microsatellites flanking the pfcrt gene had already been fixed. Presence of various Pfcrt haplotypes and a variety of intragenic microsatellites indicates that there is a wide spectrum of chloroquine resistant parasite population in India. This information should be useful for malaria control programs of the country.

Alleles↗

Spiracular indices in Anopheles stephensi: a taxonomic tool to identify ecological variants.

Thoracic spiracle length and its index was examined for their ability to discriminate two ecological variants, type form and mysorensis, of Anopheles stephensi in the adult stage. The type form is exclusively domestic in all seasons, whereas the mysorensis variant occupies the outdoor niche during monsoon and postmonsoon seasons, with spillover into domestic sites during summer ecological stress periods. A statistically significant co-relation was established between the ridge count of the egg and two adult measurements, the thoracic spiracle length, and the spiracular index. In An. stephensi type form, average spiracle length was 0.11-0.12 mm and average spiracular index was 8.09-9.23, whereas in mysorensis, the corresponding figures were 0.09-0.10 mm and 6.82-7.60. These parameters showed consistent variations in population of mosquitoes that emerged during monsoon and summer season. The thoracic lengths in both variants remained constant, and only spiracular lengths showed fluctuations in three seasonal populations. These measures provide discrimination of adult variants--identifications that are essential in malaria control programs.

Animals↗

Modification of the phenotypic expression of murine dystrophy: a morphological study.

The extensor digitorum longus muscles of 4-6-week-old normal mice (129 ReJ) and dystrophic mice (129 ReJ dy/dy) were orthotopically transplanted. Grafted muscles were examined 1, 3, 7, 14, 20, 50, and 100 days post-transplantation. The myofibers of both types of grafts underwent a similar time course of necrosis and regeneration. Other than during the initial necrotic response, no evidence of necrotic myofibers was found in either type of grafted muscle. At 100 days post-transplantation, the grafted normal and dystrophic muscles were essentially similar, except that the dystrophic graft was of smaller size. Based on a comparison of the number of myofibers found at the 100-day grafts' widest girths [631 +/- 59 SEM, for normal grafts (Bourke and Ontell, 1984); 631 +/- 74 SEM, for dystrophic grafts], it is suggested that the regenerative capability of traumatized 4-6-week-old dystrophic muscle is similar to that of traumatized normal muscle. At 100 days post-transplantation, the grafted dystrophic muscle appeared "healthier" than untraumatized muscle from age-matched dystrophic mice, having less variation in myofiber diameter, better fascicular organization, and less connective tissue. The transplantation system demonstrates the possibility of modifying the expression of genetic programming of myopathic disorders using environmental manipulation.

Animals↗

AutoPM3: enhancing variant interpretation via LLM-driven PM3 evidence extraction from scientific literature.

MOTIVATION: Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has become cost-effective, interpreting these variants-particularly collecting literature-based evidence like ACMG/AMP PM3-remains complex and time-consuming. RESULTS: We present AutoPM3, a method that automates PM3 evidence extraction from literatures using open-source large language models (LLMs). AutoPM3 combines a Text2SQL-based variant extractor and a retrieval-augmented generation (RAG) module, enhanced by a variant-specific retriever and fine-tuned LLM, to separately process tables and text. We curated PM3-Bench, a dataset of 1027 variant-publication evidence pairs from ClinGen. On openly accessible pairs, AutoPM3 achieved 86.1% accuracy for variant hits and 72.5% recall for in trans variants-outperforming other methods, including those using larger models. We uncovered the effectiveness of AutoPM3's key modules, especially for variant-specific retriever and Text2SQL, through the sequential ablation study. AutoPM3 located evidence in 76&#x2009;s, demonstrating that open-source LLMs can offer an efficient, cost-effective solution for rare disease diagnosis. AVAILABILITY AND IMPLEMENTATION: AutoPM3 is implemented and freely available under the MIT license at https://github.com/HKU-BAL/AutoPM3.

Genetic Variation↗

Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting.

SUMMARY: Graphical modeling is used to extend the gene counting method to compute maximum likelihood estimates of allele frequencies for samples of individuals related in extended pedigrees. Genotypes may be missing or partially observed, and error rates can be simultaneously estimated. AVAILABILITY: The Java classes and Javadocs pages for \mathsf\hbox GeneCountAlleles can be obtained from bioinformatics.med.utah.edu/~alun, which also has more information on its use and file formats.

Biological Evolution↗

The PowerAtlas: a power and sample size atlas for microarray experimental design and research.

BACKGROUND: Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies. RESULTS: To address this challenge, we have developed a Microrarray PowerAtlas. The atlas enables estimation of statistical power by allowing investigators to appropriately plan studies by building upon previous studies that have similar experimental characteristics. Currently, there are sample sizes and power estimates based on 632 experiments from Gene Expression Omnibus (GEO). The PowerAtlas also permits investigators to upload their own pilot data and derive power and sample size estimates from these data. This resource will be updated regularly with new datasets from GEO and other databases such as The Nottingham Arabidopsis Stock Center (NASC). CONCLUSION: This resource provides a valuable tool for investigators who are planning efficient microarray studies and estimating required sample sizes.

Algorithms↗

The relationship between the therapeutic response to risperidone and the dopamine D2 receptor polymorphism in Chinese schizophrenia patients.

Antipsychotic drugs exert both therapeutic and adverse effects through dopamine D2 receptor (DRD2) antagonism. Genetic variants of this receptor may be responsible for individual variations in neuroleptic response and may therefore be useful in predicting response. In this study we evaluated the role of six polymorphisms of the DRD2 gene in 125 risperidone-treated Chinese schizophrenia patients following the hypothesis that variation in the DRD2 gene could affect drug response. Response was categorized as a change of >40% on the Brief Psychiatric Rating Scale (BPRS). Our results show that genotyping A-241G may help to predict the efficacy of risperidone treatment on the basis that patients with the A allele showed greater improvement than those with the G allele on the overall BPRS (chi2=7.19, p=0.007, p=0.031 after correction by the program SNPSpD), while other polymorphisms, including -141C Ins/Del, TaqIB, rs1076562, T939C and TaqIA, did not show any association with the response to risperidone. These data suggest that the DRD2 A-241G polymorphism or, alternatively, another genetic variation that is in linkage disequilibrium, may influence response to risperidone in schizophrenia patients.

Adult↗

Development of sexual maturity in the ciliate Euplotes crassus: sources of variation in the timing of maturity.

The life styles of ciliated protists are particularly suitable for experimental analyses of certain aspects of developmental and genetic biology. The progression from sexual immaturity to maturity to senescence represents one of the most intriguing aspects of developmental programs. The extent to which progeny clones, their subclones, and testers used in the assay result in different lengths of immaturity has been investigated in Euplotes crassus. Six subclones from each of 12 progeny clones from a cross between stocks EC1 and EC2 were tested for maturity with stocks EC3, EC4, and EC5 on every transfer. Analysis of variance was used to partition the total variation in fissions to maturity into parts due to clones, subclones, and testers and the interactions between these levels. The error, interaction of subclones and testers, corresponds to a standard deviation of only 4.1 fissions, while the within clone within tester means range from 15.2 to 46.7 fissions; all levels except testers contribute significantly to the total variation. Most of the variability is attributable to clones (66%), the next most to error (16%), the next most to interaction of clones by testers (13%), and the least to subclones (5%). An a posteriori analysis examined whether the differences among clones were due to the cytoplasm of the clone ancestor (exconjugant), its mat (mating-type) locus genotype, or the mated pair it came from. None of these characteristics was able to interpret simply the large variability among clones. These results provide evidence that the transition from immaturity to maturity is quantitative and complex rather than a jump from one well-defined state to another.

Analysis of Variance↗