A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience

Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.

MRI Features of Histologically Diagnosed Supratentorial Primitive Neuroectodermal Tumors and Pineoblastomas in Correlation with Molecular Diagnoses and Outcomes: A Report from the Children's Oncology Group ACNS0332 Trial

BACKGROUND AND PURPOSE

Supratentorial primitive neuroectodermal tumors and pineoblastomas have traditionally been grouped together for treatment purposes. Molecular profiling of these tumors has revealed a number of distinct entities and has led to the term "CNS-primitive neuroectodermal tumors" being removed from the 2016 World Health Organization classification. The purpose of this study was to describe the MR imaging findings of histologically diagnosed primitive neuroectodermal tumors and pineoblastomas and correlate them with molecular diagnoses and outcomes.

MATERIALS AND METHODS

Histologically diagnosed primitive neuroectodermal tumors and pineoblastomas were enrolled in this Children's Oncology Group Phase III trial, and molecular classification was retrospectively completed using DNA methylation profiling. MR imaging features were systematically studied and correlated with molecular diagnoses and survival.

RESULTS

Of the 85 patients enrolled, 56 met the inclusion criteria, in whom 28 tumors were in pineal and 28 in nonpineal locations. Methylation profiling revealed a variety of diagnoses, including pineoblastomas (n = 27), high-grade gliomas (n = 17), embryonal tumors (n = 7), atypical teratoid/rhabdoid tumors (n = 3), and ependymomas (n = 2). Thus, 39% overall and 71% of nonpineal tumor diagnoses were discrepant with histopathology. Tumor location, size, margins, and edema were predictors of embryonal-versus-nonembryonal tumors. Larger size and ill-defined margins correlated with poor event-free survival, while metastatic disease by MR imaging did not.

CONCLUSIONS

In nonpineal locations, only a minority of histologically diagnosed primitive neuroectodermal tumors are embryonal tumors; therefore, high-grade glioma or ependymoma should be high on the radiographic differential. An understanding of molecularly defined tumor entities and their relative frequencies and locations will help the radiologist make more accurate predictions of the tumor types.

The economics of microgravity research

In this introduction to the economics of microgravity research, DiFrancesco and Olson explore the existing landscape and begin to define the requirements for a robust, well-funded microgravity research environment. This work chronicles the history, the opportunities, and how the decisions made today will shape the future. The past 60 years have seen tremendous growth in the capabilities and resources available to conduct microgravity science. However, we are now at an inflection point for the future of humanity in space. A confluence of factors including the rise of commercialization, a shifting funding landscape, and a growing international presence in space exploration, and terrestrial research platforms are shaping the conditions for full-scale microgravity research programs. In this first discussion, the authors focus on the concepts of markets, tangible and intangible value, research pathways and their implications for investments in research projects, and the collateral platforms needed. The opportunities and implications for adopting new approaches to funding and market-making illuminate how decisions made today will affect the speed of advances the community will be able to achieve in the future.

The effects of obesity classification method on select kinematic gait variables in adult females

AIM

Obesity has been associated with gait alterations, but most studies have utilized BMI for classification. This study examined gait alterations based on body fat and BMI.

METHOD

Participants (N.=22) had BMI and body fat percentage determined and underwent gait analysis. Body fat percentage was determined using dual energy x-ray absorptiometry (DEXA). Gait variables were examined in 3 groups: step width, preferred walking speed, and stride length; angular displacement at the knee and angular displacement at the ankle; and peak knee flexion velocity and peak knee extension velocity. A multivariate approach with follow-up univariate tests was used.

RESULTS

Based on BMI, there was a significant effect for step width, preferred walking speed, and stride length (F[3, 16]=3.47, P=0.04). Univariate tests were significant for preferred walking speed and stride length (both P<0.03). Overweight by BMI participants had a lower preferred walking speed (1.31±0.16 m/s vs. 1.53±0.18 m/s) and shorter stride length (1.23±0.11 m vs. 1.38±0.11 m). Based on body fat percentage, there was a significant effect for peak knee flexion velocity and peak knee extension velocity (F[2, 19]=4.08, P=0.03). Overweight by body fat participants had lower peak knee flexion velocity (295.99±21.32 o/s vs. 320.25±27.67 o/s; P=0.04).

CONCLUSION

Gait alterations were found for both methods of classifying obesity. However, the alterations were different for each method. The method of determining obesity appears to affect where gait alterations are found.

Concomitant requirement for Notch and Jak/Stat signaling during neuro-epithelial differentiation in the Drosophila optic lobe

The optic lobe forms a prominent compartment of the Drosophila adult brain that processes visual input from the compound eye. Neurons of the optic lobe are produced during the larval period from two neuroepithelial layers called the outer and inner optic anlage (OOA, IOA). In the early larva, the optic anlagen grow as epithelia by symmetric cell division. Subsequently, neuroepithelial cells (NE) convert into neuroblasts (NB) in a tightly regulated spatio-temporal progression that starts at the edges of the epithelia and gradually move towards its centers. Neuroblasts divide at a much faster pace in an asymmetric mode, producing lineages of neurons that populate the different parts of the optic lobe. In this paper we have reconstructed the complex morphogenesis of the optic lobe during the larval period, and established a role for the Notch and Jak/Stat signaling pathways during the NE-NB conversion. After an early phase of complete overlap in the OOA, signaling activities sort out such that Jak/Stat is active in the lateral OOA which gives rise to the lamina, and Notch remains in the medial cells that form the medulla. During the third instar, a wave front of enhanced Notch activity progressing over the OOA from medial to lateral controls the gradual NE-NB conversion. Neuroepithelial cells at the medial edge of the OOA, shortly prior to becoming neuroblasts, express high levels of Delta, which activates the Notch pathway and thereby maintains the OOA in an epithelial state. Loss of Notch signaling, as well as Jak/Stat signaling, results in a premature NE-NB conversion of the OOA, which in turn has severe effects on optic lobe patterning. Our findings present the Drosophila optic lobe as a useful model to analyze the key signaling mechanisms controlling transitions of progenitor cells from symmetric (growth) to asymmetric (differentiative) divisions.

"Deconstructing" scientific research: a practical and scalable pedagogical tool to provide evidence-based science instruction

Focused analysis of current research projects provides an effective platform for teaching early-stage undergraduates the logic of scientific inquiry.

G-TRACE: rapid Gal4-based cell lineage analysis in Drosophila

We combine Gal4/UAS, FLP/FRT and fluorescent reporters to generate cell clones that provide spatial, temporal, and genetic information about the origins of individual cells in Drosophila. We name this combination the Gal4 Technique for Real-time and Clonal Expression (G-TRACE). The approach should allow for screening and the identification of real-time and lineage-traced expression patterns on a genomic scale.

Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes

Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes.

Structure of Sla1p homology domain 1 and interaction with the NPFxD endocytic internalization motif

Adaptor proteins play important endocytic roles including recognition of internalization signals in transmembrane cargo. Sla1p serves as the adaptor for uptake of transmembrane proteins containing the NPFxD internalization signal, and is essential for normal functioning of the actin cytoskeleton during endocytosis. The Sla1p homology domain 1 (SHD1) within Sla1p is responsible for recognition of the NPFxD signal. This study presents the NMR structure of the NPFxD-bound state of SHD1 and a model for the protein-ligand complex. The alpha+beta structure of the protein reveals an SH3-like topology with a solvent-exposed hydrophobic ligand binding site. NMR chemical shift perturbations and effects of structure-based mutations on ligand binding in vitro define residues that are key for NPFxD binding. Mutations that abolish ligand recognition in vitro also abolish NPFxD-mediated receptor internalization in vivo. Thus, SHD1 is a novel functional domain based on SH3-like topology, which employs a unique binding site to recognize the NPFxD endocytic internalization signal. Its distant relationship with the SH3 fold endows this superfamily with a new role in endocytosis.

Growth rate, protein accumulation, and catabolic enzyme activity of skeletal muscles of galliform birds

We measured the mass and several potential indices of functional capacity of the leg and pectoral muscles through 21 d of age in chicks of three species of galliform birds and the domesticated turkey. The study was conducted to test the hypothesis that the growth rate of a tissue is inversely related to its capacity for mature function across species. We measured the proportion of protein and the activities of the catabolic enzymes citrate synthase (CS), pyruvate kinase (PK), and beta -hydroxy-acyl-CoA-dehydrogenase (HOAD) and estimated exponential growth rate (EGR) from growth increments. EGR was negatively related to proportion of protein, PK, and HOAD and positively related to CS activity. In a multiple regression, EGR was uniquely related only to proportion of protein; it was higher in pectoral muscles and increased in this order: wild turkey<pheasant<domestic turkey<chukar. Thus, among wild species, the muscles of smaller species grew more rapidly for a given proportion of protein, but domestication and selection for rapid growth and large muscle size in turkeys resulted in substantially elevated growth rate. When the proportion of protein was normalized by its maximum value for each species and muscle type, the relationship between EGR and normalized protein did not differ significantly among species or muscle type. Thus, if we accept the proportion of protein relative to the mature level as an index of functional capacity--presumably representing the assembly of the contractile apparatus--then growth rate is consistently inversely related to a muscle's capacity for mature function, that is, force generation.

Photosynthesis in the Archean era

The earliest reductant for photosynthesis may have been H2. The carbon isotope composition measured in graphite from the 3.8-Ga Isua Supercrustal Belt in Greenland is attributed to H2-driven photosynthesis, rather than to oxygenic photosynthesis as there would have been no evolutionary pressure for oxygenic photosynthesis in the presence of H2. Anoxygenic photosynthesis may also be responsible for the filamentous mats found in the 3.4-Ga Buck Reef Chert in South Africa. Another early reductant was probably H2S. Eventually the supply of H2 in the atmosphere was likely to have been attenuated by the production of CH4 by methanogens, and the supply of H2S was likely to have been restricted to special environments near volcanos. Evaporites, possible stromatolites, and possible microfossils found in the 3.5-Ga Warrawoona Megasequence in Australia are attributed to sulfur-driven photosynthesis. Proteobacteria and protocyanobacteria are assumed to have evolved to use ferrous iron as reductant sometime around 3.0 Ga or earlier. This type of photosynthesis could have produced banded iron formations similar to those produced by oxygenic photosynthesis. Microfossils, stromatolites, and chemical biomarkers in Australia and South Africa show that cyanobacteria containing chlorophyll a and carrying out oxygenic photosynthesis appeared by 2.8 Ga, but the oxygen level in the atmosphere did not begin to increase until about 2.3 Ga.

Step structures on III-V phosphide (001) surfaces: how do steps and Sb affect CuPt ordering of GaInP2?

The observation of III-V phosphide (001)-(2 x 2) surfaces makes it possible to solve a long standing mystery of step structures. First-principles calculations show that a bulklike type-B step on a hydrogenated 2 x 2 surface is more stable than a rebonded one by 1.1 eV/unit step. In contrast, this energy difference for a H-free beta(2 x 4) surface is only 0.5 eV/unit step. The large difference explains why the CuPt ordering of GaInP is stronger in metal-organic chemical vapor deposition than in molecular beam epitaxy. However, a minute amount of Sb will preferentially attach to the 2 x 2 surface steps and induce additional step structures that cause ordering disruption.

Thinking about the evolution of photosynthesis

Photosynthesis is an ancient process on Earth. Chemical evidence and recent fossil finds indicate that cyanobacteria existed 2.5-2.6 billion years (Ga) ago, and these were certainly preceded by a variety of forms of anoxygenic photosynthetic bacteria. Carbon isotope data suggest autotrophic carbon fixation was taking place at least a billion years earlier. However, the nature of the earliest photosynthetic organisms is not well understood. The major elements of the photosynthetic apparatus are the reaction centers, antenna complexes, electron transfer complexes and carbon fixation machinery. These parts almost certainly have not had the same evolutionary history in all organisms, so that the photosynthetic apparatus is best viewed as a mosaic made up of a number of substructures each with its own unique evolutionary history. There are two schools of thought concerning the origin of reaction centers and photosynthesis. One school pictures the evolution of reaction centers beginning in the prebiotic phase while the other school sees reaction centers evolving later from cytochrome b in bacteria. Two models have been put forth for the subsequent evolution of reaction centers in proteobacteria, green filamentous (non-sulfur) bacteria, cyanobacteria, heliobacteria and green sulfur bacteria. In the selective loss model the most recent common ancestor of all subsequent photosynthetic systems is postulated to have contained both RC1 and RC2. The evolution of reaction centers in proteobacteria and green filamentous bacteria resulted from the loss of RC1, while the evolution of reaction centers in heliobacteria and green sulfur bacteria resulted from the loss of RC2. Both RC1 and RC2 were retained in the cyanobacteria. In the fusion model the most recent common ancestor is postulated to have given rise to two lines, one containing RC1 and the other containing RC2. The RC1 line gave rise to the reaction centers of heliobacteria and green sulfur bacteria, and the RC2 line led to the reaction centers of proteobacteria and green filamentous bacteria. The two reaction centers of cyanobacteria were the result of a genetic fusion of an organism containing RC1 and an organism containing RC2. The evolutionary histories of the various classes of antenna/light-harvesting complexes appear to be completely independent. The transition from anoxygenic to oxygenic photosynthesis took place when the cyanobacteria learned how to use water as an electron donor for carbon dioxide reduction. Before that time hydrogen peroxide may have served as a transitional donor, and before that, ferrous iron may have been the original source of reducing power.

The FMO Protein

In this article I review the history of research on the Fenna-Matthews-Olson (FMO) protein with emphasis on my contributions. The FMO protein, which transfers energy from the chlorosome to the reaction center in green sulfur bacteria, was discovered in 1962 and shown to contain bacteriochlorophyll a. From the absorption and circular dichroism spectra, it was clear that there was an exciton interaction between the bacteriochlorophyll molecules. Low temperature spectra indicated a seven-fold exciton splitting of the Q(y) band. The FMO protein was crystallized in 1964, and the X-ray structure determined in 1979 by B.W. Matthews, R.E. Fenna, M.C. Bolognesi, M.F. Schmidt and J.M. Olson. The structure showed that the protein consisted of three subunits, each containing seven bacteriochlorophyll molecules. The optical spectra were satisfactorily simulated in 1997. In living cells the FMO protein is located between the chlorosome and the reaction centers with the C3 symmetry axis perpendicular to the membrane. The FMO protein may be related to PscA in the reaction center.

Expression of the murine CB2 cannabinoid receptor using a recombinant Semliki Forest virus

A recombinant Semliki Forest virus (SFV) RNA construct, SFV1-mCB(2) RNA, was employed for the high-level expression of the murine CB(2) (mCB(2)) cannabinoid receptor in baby hamster kidney cells. Biosynthetic radiolabel incorporation studies in concert with urea-sodium dodecylsulfate-polyacrylamide gel electrophoresis (urea-SDS-PAGE) and western immunoblotting revealed that two major proteins of approximately 26 and 40kDa were produced by the construct. The 40kDa product, but not the 26kDa product, was glycosylated as determined by 2-deoxy-D-glucose incorporation and peptide-N-glycosidase F digestion analysis. Assessment of [3H]CP55940 ([3H]-(-)-cis-3-[2-hydroxy-4-(1,1-dimethylheptyl)phenyl]-trans-4-(3-hydroxypropyl)cyclohexanol) binding data for membranes of cells transfected with SFV1-mCB(2) RNA indicated a K(d) of 0.35+/-0.04nM and a B(max) of 24.4+/-2.7pmol/mg. A rank order of binding affinities for cannabinoids, which paralleled that reported for native mCB(2) receptors, was observed. The CB(2) receptor-specific antagonist SR144528 (N-[(1S)-endo-1,3,3-trimethyl bicyclo[2.2.1]heptan-2-yl]-5-(4-chloro-3-methylphenyl)-1-(4-methylbenzyl)-pyrazole-3-carboxamide) blocked binding of [3H]CP55940, while the CB(1) receptor-specific antagonist SR141716A [N-(piperidin-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide hydrochloride] had a minimal effect. These results indicate that the recombinant receptor expressed from SFV1-mCB(2) RNA exhibits properties, including ligand binding features, that are consistent with those for the native mCB(2) receptor. However, the presence of both 26 and 40kDa receptor species is consistent with alternative translation from two AUG start sites using the SFV1-mCB(2) RNA expression system.

The FMO protein is related to PscA in the reaction center of green sulfur bacteria

The Fenna-Matthews-Olson protein is a water-soluble protein found only in green sulfur bacteria. Each subunit contains seven bacteriochlorophyll (BChl) a molecules wrapped in a string bag of protein consisting of mostly beta sheet. Most other chlorophyll-binding proteins are water-insoluble proteins containing membrane-spanning alpha helices. We compared an FMO consensus sequence to well-characterized, membrane-bound chlorophyll-binding proteins: L & M (reaction center proteins of proteobacteria), D1 & D2 (reaction center proteins of PS II), CP43 & CP47 (core proteins of PS II), PsaA & PsaB (reaction center proteins of PS I), PscA (reaction center protein of green sulfur bacteria), and PshA (reaction center protein of heliobacteria). We aligned the FMO sequence with the other sequences using the PAM250 matrix modified for His binding-site identities and found a signature sequence (LxHHxxxGxFxxF) common to FMO and PscA. (The two His residues are BChl a. binding sites in FMO.) This signature sequence is part of a 220-residue C-terminal segment with an identity score of 13%. PRSS (Probability of Random Shuffle) analysis showed that the 220-residue alignment is better than 96% of randomized alignments. This evidence supports the hypothesis that FMO protein is related to PscA.

A genome screen of systemic lupus erythematosus using affected-relative-pair linkage analysis with covariates demonstrates genetic heterogeneity

Systemic lupus erythematosus (SLE) appears to be the consequence of complex genetics and of only partly understood environmental contributions. Previous work by ourselves and by others has established genetic effects on 1q, 2q, 4p, 6p, and 16p using SLE as the phenotype. However, individual SLE affecteds are extraordinarily different from one another by clinical and laboratory measures. This variation may have a genetic basis; if so, it is advantageous to incorporate measures of between-family clinical variability as covariates in a genetic linkage analysis of affected relative pairs (ARPs) to allow for locus heterogeneity. This approach was applied to genome scan marker data from 160 pedigrees multiplex for SLE and containing 202 ARPs. Because the number of potential covariates was large, we used both ad hoc methods and formal principal components analysis to construct four composite covariates using the SLE classification criteria plus age of onset, ethnicity, and sex. Linkage analysis without covariates has detected evidence for linkage at 1q22-24, 2q37, 4p16, 12p12-11, and 17p13. Linkage analysis with these covariates uncovered linkage at 13p11, 17q11-25, and 20q12 and greatly improved evidence for linkage at 1q22-24, 2q37, 12p12-11, and 17p13. Follow-up analysis identified the original variables contributing to locus heterogeneity in each of these locations. In conclusion, allowing for locus heterogeneity through the incorporation of covariates in linkage analysis is a useful way to dissect the genetic contributions to SLE and uncover new genetic effects.

Strain-driven mesoscopic reconstruction of the As/Ge(111) surface

Periodic arrays of large hexagonal tiles (up to 170 A in size) are observed on As/Ge(111) surfaces. First-principles total energy calculations combined with scanning tunneling microscopy reveal a (5-7-5)-ringed structure for the trenches that separate the tiles. We find that trenches form via an exothermic process. The calculated equilibrium trench spacing of approximately 104 A agrees with experiment. Comparison between first-principles calculations and continuum elasticity theory suggests that the observed mesoscopic reconstruction is driven entirely by long-range surface strain relaxation.

Locating the genes underlying a simulated complex disease by discriminant analysis

The purpose of this study was to propose and evaluate a novel multivariate approach for genetic mapping of complex binary human diseases. This approach uses the application of either of two methods of standard (stepwise) discriminant analysis to detect linkage based on the differential marker identity-by-descent distributions among the three affection groups of sib pairs (concordantly affected, discordant, and concordantly unaffected). One of the advantages of this approach is that it allows for simultaneously testing all markers, as well as other genetic and environmental factors, in a single multivariate setting. We have explored its properties and behaviors via an application to the simulated data in Genetic Analysis Workshop 12.

Comparison of three methods for obtaining principal components from family data in genetic analysis of complex disease

Three multivariate techniques used to derive principal components (PCs) from family data were compared for their ability to model family data and power to detect linkage. Using the simulated data from Genetic Analysis Workshop 12, the five quantitative traits were first adjusted for age, sex, and environmental factors 1 and 2. Then, standard PCs, PCs obtained from between-family covariance, and PCs obtained from within-family genetic covariance were derived and subjected to multivariate sib pair linkage analysis. The standard PCs obtained from the overall correlation matrix allowed identification of key features of the true genetic model more readily than did the other methods. For detection of linkage, standard PCs and PCs obtained from the between-family genetic covariance performed similarly in terms of both power and type 1 error, and both methods performed better than the PCs obtained from within-family genetic covariance.

Sla1p serves as the targeting signal recognition factor for NPFX(1,2)D-mediated endocytosis

Efficient endocytosis requires cytoplasmic domain targeting signals that specify incorporation of cargo into endocytic vesicles. Adaptor proteins play a central role in cargo collection by linking targeting signals to the endocytic machinery. We have characterized NPFX(1,2) (NPFX[1,2]D) targeting signals and identified the actin-associated protein Sla1p as the adaptor for NPFX(1,2)D-mediated endocytosis in Saccharomyces cerevisiae. 11 amino acids encompassing an NPFX(1,2)D sequence were sufficient to direct uptake of a truncated form of the pheromone receptor Ste2p. In this context, endocytic targeting activity was not sustained by conservative substitutions of the phenylalanine or aspartate. An NPFX1,2D-related sequence was identified in native Ste2p that functions redundantly with ubiquitin-based endocytic signals. A two-hybrid interaction screen for NPFX(1,2)D-interacting proteins yielded SLA1, but no genes encoding Eps15 homology (EH) domains, protein modules known to recognize NPF peptides. Furthermore, EH domains did not recognize an NPFX(1,2)D signal when directly tested by two-hybrid analysis. SLA1 disruption severely inhibited NPFX(1,2)D-mediated endocytosis, but only marginally affected ubiquitin-directed uptake. NPFX(1,2)D-dependent internalization required a conserved domain of Sla1p, SLA1 homology domain, which selectively bound an NPFX(1,2)D-containing fusion protein in vitro. Thus, through a novel NPF-binding domain, Sla1p serves as an endocytic targeting signal adaptor, providing a means to couple cargo with clathrin- and actin-based endocytic machineries.

Linkage analysis of human systemic lupus erythematosus-related traits: a principal component approach

OBJECTIVE

To identify chromosomal regions containing genes involved in the susceptibility to human systemic lupus erythematosus (SLE)-related traits.

METHODS

In the context of a genome scan, we analyzed 101 SLE-affected sibpairs with respect to dermatologic, renal, immunologic, hematologic, neurologic, cardiopulmonary, and arthritic characteristics. Phenotypes were redefined in terms of principal components, which are synthetic variables composed of linear combinations of the original traits. Using 9 principal components obtained from these 7 traits plus age at SLE onset and race, we analyzed genome scan data with the multivariate version of the new Haseman-Elston regression model.

RESULTS

The largest linkage for an individual trait was on chromosome 2 at 228 cM (immunologic; P = 0.00048). The most significant linkage to an individual principal component was on chromosome 4 at 208 cM (P = 0.00007). The largest multivariate linkage was on chromosome 7 at 69 cM (P = 0.0001). Of the individual organ systems, dermatologic involvement had the largest effect (P = 0.0083) at this peak at 7p13 on chromosome 7. Further analyses revealed that malar rash, a subtype of dermatologic involvement, was linked significantly (P = 0.00458) to this location.

CONCLUSION

These results provide evidence of the presence and locations of genes that are involved in the genetic susceptibility to SLE-related traits in humans.

Altered transcription in yeast expressing expanded polyglutamine

Expanded polyglutamine tracts are responsible for at least eight fatal neurodegenerative diseases. In mouse models, proteins with expanded polyglutamine cause transcriptional dysregulation before onset of symptoms, suggesting that this dysregulation may be an early event in polyglutamine pathogenesis. Transcriptional dysregulation and cellular toxicity may be due to interaction between expanded polyglutamine and the histone acetyltransferase CREB-binding protein. To determine whether polyglutamine-mediated transcriptional dysregulation occurs in yeast, we expressed polyglutamine tracts in Saccharomyces cerevisiae. Gene expression profiles were determined for strains expressing either a cytoplasmic or nuclear protein with 23 or 75 glutamines, and these profiles were compared to existing profiles of mutant yeast strains. Transcriptional induction of genes encoding chaperones and heat-shock factors was caused by expression of expanded polyglutamine in either the nucleus or cytoplasm. Transcriptional repression was most prominent in yeast expressing nuclear expanded polyglutamine and was similar to profiles of yeast strains deleted for components of the histone acetyltransferase complex Spt/Ada/Gcn5 acetyltransferase (SAGA). The promoter from one affected gene (PHO84) was repressed by expanded polyglutamine in a reporter gene assay, and this effect was mitigated by the histone deacetylase inhibitor, Trichostatin A. Consistent with an effect on SAGA, nuclear expanded polyglutamine enhanced the toxicity of a deletion in the SAGA component SPT3. Thus, an early component of polyglutamine toxicity, transcriptional dysregulation, is conserved in yeast and is pharmacologically antagonized by a histone deacetylase inhibitor. These results suggest a therapeutic approach for treatment of polyglutamine diseases and provide the potential for yeast-based screens for agents that reverse polyglutamine toxicity.

Steps on As-terminated Ge(001) revisited: theory versus experiment

We examine the double-layer B-type steps on As-terminated vicinal Ge(001) surfaces. The currently accepted structure is a chemically inert bulklike structure without any gap state, and with all the chemical bonds of the Ge and As atoms being satisfied. However, we show that the need for optimizing the p(3) pyramidal angles of the threefold coordinated As atoms drives unusual atomic rearrangement. This leads to a more stable reconstruction involving odd-membered (5-7-5) rings at the step edge. Comparison between theoretical and experimental scanning tunneling microscopy images yields excellent agreement.

The amyloid precursor protein locus and very-late-onset Alzheimer disease

Although mutations in the amyloid-beta precursor protein (APP) gene are known to confer high risk of Alzheimer disease (AD) to a small percentage of families in which it has early onset, convincing evidence of a major role for the APP locus in late-onset AD has not been forthcoming. In this report, we have used a covariate-based affected-sib-pair linkage method to analyze the chromosome 21 clinical and genetic data obtained on affected sibships by the National Institute of Mental Health Alzheimer Disease Genetics Initiative. The baseline model (without covariates) gave a LOD score of 0.02, which increases to 1.43 when covariates representing the additive effects of E2 and E4 are added. Larger increases in LOD scores were found when age at last examination/death (LOD score 5.54; P=.000002) or age at onset plus disease duration (LOD score 5.63; P=.000006) were included in the linkage model. We conclude that the APP locus may predispose to AD in the very elderly.

Ontogeny of catabolic and morphological properties of skeletal muscle of the red-winged blackbird (Agelaius phoeniceus)

Thermogenic capabilities of red-winged blackbirds improve markedly during their 10-12-day nestling period, especially between day 5 and day 8. The time course of improvements may be determined by the maturation of skeletal muscles involved in shivering thermogenesis, particularly the pectoralis muscles. To test this hypothesis, morphological and biochemical changes in pectoral and leg muscles were measured in young and adult blackbirds. Both muscles grew disproportionately relative to body mass. The pectoralis consisted entirely of fast-twitch fibers, predominantly fast oxidative glycolytic. In contrast, the gastrocnemius muscle consisted of a mixture of slow and fast fibers (predominantly fast glycolytic). Although fiber composition was constant, both cross-sectional area and density of fibers increased with age in both muscles. Catabolic capacities of the pectoralis increased significantly (approximately 7-8-fold) throughout the nestling period, most abruptly after day 3 (citrate synthase, CS) or day 4 (3-hydroxacyl-CoA-dehydrogenase, HOAD). Myofibrillar ATPase activities in the pectoralis were initially low, but increased after day 5. Further increases in CS and myofibrillar ATPase activities occurred in the pectoralis after fledging. CS and HOAD activities in the leg were much lower, but myofibrillar ATPase activities were remarkably similar in the two muscles, differing only in adults. These results are consistent with the hypothesis that the development of endothermy is dependent on the morphological and biochemical maturation of skeletal muscles important in thermogenesis.

No excess of early onset cancer in family members of Wilms tumor patients

BACKGROUND

Wilms tumor is one of the few pediatric cancers with well-defined familial and genetic components. The authors assessed the risk of early-onset cancers in first- and second-degree relatives of patients enrolled by the National Wilms Tumor Study Group.

METHODS

Using a stratified sampling scheme that targeted 530 families of patients who were believed a priori to have a genetic contribution to their disease, the authors conducted interviews regarding cancer occurrence in 4258 family members from 296 families of patients with Wilms tumor. Reports of malignant neoplasms that occurred before 55 years of age were confirmed by review of medical records wherever possible. A period of risk was defined for each family member based on calendar time and his or her relationship to the proband.

RESULTS

Ninety-nine cancers were observed, whereas 126.8 were expected by applying standard cancer rates for age and calendar period to the 120,885 person-years at risk. The standardized incidence ratio (SIR) was O-E = 0.78 with 95% confidence interval (CI) of (0.64, 0.95). In subgroup analyses, the highest relative risks were observed for parents of the index case (O/E = 21/13.0 = 1.6, 95% CI = 1.0, 2.5) and for leukemia (O/E = 9/4.9 = 1.9, 95% CI= 0.85,3.5).

CONCLUSIONS

The results of this study may provide reassurance to families of children who have had Wilms tumor. Potential sources of bias included the low (56%) rate of participation of targeted families. In general, the biases might have led to the underreporting of some cancers, especially in more distant relatives. The possibility of a slight excess of cancer in parents of Wilms tumor patients could not be excluded.

An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles

We have developed a statistical regression modeling approach to discover genes that are differentially expressed between two predefined sample groups in DNA microarray experiments. Our model is based on well-defined assumptions, uses rigorous and well-characterized statistical measures, and accounts for the heterogeneity and genomic complexity of the data. In contrast to cluster analysis, which attempts to define groups of genes and/or samples that share common overall expression profiles, our modeling approach uses known sample group membership to focus on expression profiles of individual genes in a sensitive and robust manner. Further, this approach can be used to test statistical hypotheses about gene expression. To demonstrate this methodology, we compared the expression profiles of 11 acute myeloid leukemia (AML) and 27 acute lymphoblastic leukemia (ALL) samples from a previous study (Golub et al. 1999) and found 141 genes differentially expressed between AML and ALL with a 1% significance at the genomic level. Using this modeling approach to compare different sample groups within the AML samples, we identified a group of genes whose expression profiles correlated with that of thrombopoietin and found that genes whose expression associated with AML treatment outcome lie in recurrent chromosomal locations. Our results are compared with those obtained using t-tests or Wilcoxon rank sum statistics.

NeuroD2 is necessary for development and survival of central nervous system neurons

NeuroD2 is sufficient to induce cell cycle arrest and neurogenic differentiation in nonneuronal cells. To determine whether this bHLH transcription factor was necessary for normal brain development, we used homologous recombination to replace the neuroD2 coding region with a beta-galactosidase reporter gene. The neuroD2 gene expressed the reporter in a subset of neurons in the central nervous system, including in neurons of the neocortex and hippocampus and cerebellum. NeuroD2(-/-) mice showed normal development until about day P14, when they began exhibiting ataxia and failure to thrive. Brain areas that expressed neuroD2 were smaller than normal and showed higher rates of apoptosis. Cerebella of neuroD2-null mice expressed reduced levels of genes encoding proteins that support cerebellar granule cell survival, including brain-derived neurotrophic factor (BDNF). Decreased levels of BDNF and higher rates of apoptosis in cerebellar granule cells of neuroD2(-/-) mice indicate that neuroD2 is necessary for the survival of specific populations of central nervous system neurons in addition to its known effects on cell cycle regulation and neuronal differentiation.

The heritability of attitudes: a study of twins

The genetic basis of individual differences in attitudes was examined in a survey of 195 pairs of monozygotic twins and 141 pairs of same-sex dizygotic twins. A principal components analysis of the 30 attitude items in the survey identified 9 attitude factors, of which 6 yielded significant heritability coefficients. Nonshared environmental factors accounted for the most variance in the attitude factors. Possible mediators of attitude heritability were also assessed, including personality traits, physical characteristics, and academic achievement. Analyses showed that several of these possible mediators correlated at a genetic level with the heritable attitude factors, suggesting that the heritability of the mediator variables might account for part of the heritable components of some attitudes. There was also some evidence that highly heritable attitudes were psychologically "stronger" than less heritable attitudes.

Model-free linkage analysis with covariates confirms linkage of prostate cancer to chromosomes 1 and 4

As with many complex genetic diseases, genome scans for prostate cancer have given conflicting results, often failing to provide replication of previous findings. One factor contributing to the lack of consistency across studies is locus heterogeneity, which can weaken or even eliminate evidence for linkage that is present only in a subset of families. Currently, most analyses either fail to account for locus heterogeneity or attempt to account for it only by partitioning data sets into smaller and smaller portions. In the present study, we model locus heterogeneity among affected sib pairs with prostate cancer by including covariates in the linkage analysis that serve as surrogate measures of between-family linkage differences. The model is a modification of the Olson conditional logistic model for affected relative pairs. By including Gleason score, age at onset, male-to-male transmission, and/or number of affected first-degree family members as covariates, we detected linkage near three locations that were previously identified by linkage (1q24-25 [HPC1; LOD score 3.25, P=.00012], 1q42.2-43 [PCAP; LOD score 2.84, P=.0030], and 4q [LOD score 2.80, P=.00038]), near the androgen-receptor locus on Xq12-13 (AR; LOD score 3.06, P=.00053), and at five new locations (LOD score > 2.5). Without covariates, only a few weak-to-moderate linkage signals were found, none of which replicate findings of previous genome scans. We conclude that covariate-based linkage analysis greatly improves the likelihood that linked regions will be found by incorporation of information about heterogeneity within the sample.

Therapeutic opportunities in polyglutamine disease

Polyglutamine diseases comprise a class of familial neurodegenerative disorders caused by expression of proteins containing expanded polyglutamine tracts. Great progress has been made in elucidating the molecular mechanisms contributing to polyglutamine pathology, and in identifying potential drug targets. Although much remains to be learned, these advances provide an opportunity for rational approaches to target-based drug discovery.

A novel UDP-glucose transferase is part of the callose synthase complex and interacts with phragmoplastin at the forming cell plate

Using phragmoplastin as a bait, we isolated an Arabidopsis cDNA encoding a novel UDP-glucose transferase (UGT1). This interaction was confirmed by an in vitro protein--protein interaction assay using purified UGT1 and radiolabeled phragmoplastin. Protein gel blot results revealed that UGT1 is associated with the membrane fraction and copurified with the product-entrapped callose synthase complex. These data suggest that UGT1 may act as a subunit of callose synthase that uses UDP-glucose to synthesize callose, a 1,3-beta-glucan. UGT1 also interacted with Rop1, a Rho-like protein, and this interaction occurred only in its GTP-bound configuration, suggesting that the plant callose synthase may be regulated by Rop1 through the interaction with UGT1. The green fluorescent protein--UGT1 fusion protein was located on the forming cell plate during cytokinesis. We propose that UGT1 may transfer UDP-glucose from sucrose synthase to the callose synthase and thus help form a substrate channel for the synthesis of callose at the forming cell plate.

Catabolic capacity of the muscles of shorebird chicks: maturation of function in relation to body size

Newly hatched precocial chicks of arctic shorebirds are able to walk and regulate their body temperatures to a limited extent. Yet, they must also grow rapidly to achieve independence before the end of the short arctic growing season. A rapid growth rate may conflict with development of mature function, and because of the allometric scaling of thermal relationships, this trade-off might be resolved differently in large and small species. We assessed growth (mass) and functional maturity (catabolic enzyme activity) in leg and pectoral muscles of chicks aged 1-16 d and adults of two scolopacid shorebirds, the smaller dunlin (Calidris alpina: neonate mass 8 g, adult mass 50 g) and larger whimbrel (Numenius phaeopus; neonate mass 34 g, adult mass 380 g). Enzyme activity indicates maximum catabolic capacity, which is one aspect of the development of functional maturity of muscle. The growth rate-maturity hypothesis predicts that the development of catabolic capacity should be delayed in faster-growing muscle masses. Leg muscles of both species were a larger proportion of adult size at hatching and grew faster than pectoral muscles. Pectoral muscles grew more rapidly in the dunlin than in the whimbrel, whereas leg muscles grew more rapidly in the whimbrel. In both species and in both leg and pectoral muscles, enzyme activities generally increased with age, suggesting increasing functional maturity. Levels of citrate synthase activity were similar to those reported for other species, but l-3-hydroxyacyl-CoA-dehydrogenase and pyruvate kinase (PK) activities were comparatively high. Catabolic capacities of leg muscles were initially high compared to those of pectoral muscles, but with the exception of glycolytic (PK) capacities, these subsequently increased only modestly or even decreased as chicks grew. The earlier functional maturity of the more rapidly growing leg muscles, as well as the generally higher functional maturity in muscles of the more rapidly growing dunlin chicks, contradicts the growth rate-maturity function trade-off and suggests that birds have considerable latitude to modify this relationship. Whimbrel chicks, apparently, can rely on allometric scaling of power requirements for locomotion and the thermal inertia of their larger mass to reduce demands on their muscles, whereas dunlin chicks require muscles with higher metabolic capacity from an earlier age. Thus, larger and smaller species may adopt different strategies of growth and tissue maturation.

A family-based strategy to identify genes for diabetic nephropathy

Diabetic nephropathy (DN) clusters in families and specific ethnic groups, suggesting a genetic basis of disease transmission. Identification of DN susceptibility loci should reveal new therapeutic targets but requires accurate phenotyping. A powerful family-based strategy, which is novel to the pursuit of nephropathy genes in type 2 diabetes, is being used to collect a sample for candidate gene and genome scan analyses. Sib pairs that include DN index cases plus (1) sibs concordant for type 2 diabetes and DN (affected sib pairs [ASPs]) and (2) sibs concordant for type 2 diabetes but discordant for DN (discordant sib pairs [DSPs]) are targeted specifically for recruitment. Type 2 diabetes and DN phenotype criteria for index cases include diabetes onset after 38 years of age, duration 10 years or longer, no initial insulin treatment, diabetic retinopathy, end-stage renal disease (ESRD), and history of nephrotic proteinuria. ESRD patients were screened by questionnaire and medical record review (n = 2114). Of 666 patients with ESRD secondary to DN, 227 had a family history of ESRD, 150 had a living diabetic sib, and 124 families were enrolled. Sixty-five families, with 86 diabetic relative pairs (69 sibs, 17 children), have been completely phenotyped. If nephropathy in diabetic sibs is defined as albuminuria greater than 0.3 g/24 h, 31 ASPs and 26 DSPs (diabetic sib with albuminuria <0.3 g/24 h) were identified. Applying more stringent criteria, only 12 ASPs (sib with diabetes >10 years, diabetic retinopathy, and nephrotic proteinuria) and 9 DSPs (sib with diabetes >10 years and normal urine albumin excretion) were identified. Extrapolating from the number of subjects recruited using stringent phenotyping criteria, nearly 10,000 ESRD patients are required for screening to achieve adequate statistical power for linkage analysis (80% power to detect locus-specific relative risk of 2.2 at a lod score of 3.0). Careful phenotyping requires a large recruitment effort but is necessary to reduce population heterogeneity, a strategy that increases the likelihood of identifying DN loci.

;Evolution of Photosynthesis' (1970), re-examined thirty years later

I have re-examined my 1970 article 'Evolution of Photosynthesis' (Olson JM, Science 168: 438-446) to see whether any of my original proposals still survive. My original conviction that the evolution of photosynthesis was intimately connected with the origin of life has been replaced with the realization that photosynthesis may have been invented by the Bacteria after their divergence from the Archea. The common ancestor of all extant photosynthetic bacteria and cyanobacteria probably contained bacteriochlorophyll a, rather than chlorophyll a as originally proposed, and may have carried out CO(2) fixation instead of photoassimilation. The first electron donors were probably reduced sulfur compounds and later ferrous iron. The common ancestor of all extant reaction centers was probably similar to the homodimeric RC1 of present-day green sulfur bacteria (Chlorobiaceae) and heliobacteria. In the common ancestor of proteobacteria and cyanobacteria, the gene for the primordial RC1 was apparently duplicated and one copy split into two genes, one for RC2 and the other for a chlorophyll protein similar to CP43 and CP47 in extant cyanobacteria and chloroplasts. Homodimeric RC1 and homodimeric RC2 functioned in series as in the Z-scheme to deliver electrons from Fe(OH)(+) to NADP(+), while RC1 and/or RC2 separately drove cyclic electron flow for the production of ATP. In the line of evolution leading to proteobacteria, RC1 and the chlorophyll protein were lost, but RC2 was retained and became heterodimeric. In the line leading to cyanobacteria, both RC1 and RC2 replaced bacteriochlorophyll a with chlorophyll a and became heterodimeric. Heterodimeric RC2 further coevolved with a Mn-containing complex to utilize water as the electron donor for CO(2) fixation. The chlorophyll-protein was also retained and evolved into CP43 and CP47. Heliobacteria are the nearest photosynthetic relatives of cyanobacteria. The branching order of photosynthetic genes appears to be (1) proteobacteria, (2) green bacteria (Chlorobiaceae plus Chloroflexaceae), and (3) heliobacteria plus cyanobacteria.

Genome scan of human systemic lupus erythematosus by regression modeling: evidence of linkage and epistasis at 4p16-15.2

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder involving at least hormonal, environmental, and genetic factors. Familial aggregation, a 2%-3% sibling recurrence rate, monozygotic twin concordance >20%, association with several candidate genes, as well as the results of five genome scans support a genetic component. We present here the results of a genome scan of 126 pedigrees multiplex for SLE, including 469 sibling pairs (affected and unaffected) and 175 affected relative pairs. Using the revised multipoint Haseman-Elston regression technique for concordant and discordant sibling pairs and a conditional logistic regression technique for affected relative pairs, we identify a novel linkage to chromosome 4p16-15.2 (P=.0003 and LOD=3.84) and present evidence of an epistatic interaction between chromosome 4p16-15.2 and chromosome 5p15 in our European American families. We confirm the evidence of linkage to chromosome 4p16-15.2 in European American families using data from an independent pedigree collection. In addition, our data support the published results of three independent studies for nine purportedly linked regions and agree with the previously published results from a subset of these data for three regions. In summary, results from two new analytical techniques establish and confirm linkage with SLE at 4p16-15.2, indicate epistasis between 4p16-15.2 and 5p15, and confirm other linkage effects with SLE that have been reported elsewhere.

Ascertainment adjustment: where does it take us?

It is commonly assumed that the parameter estimates of a statistical genetics model that has been adjusted for ascertainment will estimate parameters in the general population from which the ascertained subpopulation was originally drawn. We show that this is true only in certain restricted circumstances. More generally, ascertainment-adjusted parameter estimates reflect parameters in the ascertained subpopulation. In many situations, this shift in perspective is immaterial: the parameters of interest are the same in the ascertained sample and in the population from which it was drawn, and it is therefore irrelevant to which population inferences are presumed to apply. In other circumstances, however, this is not so. This has important implications, particularly for studies investigating the etiology of complex diseases.

Haseman and Elston revisited

Haseman and Elston (H-E) [1972] proposed a method to detect quantitative trait loci by linkage to a marker. The squared sib-pair trait difference is regressed on the proportion of marker alleles the pair is estimated to share identical by descent: a significantly negative regression coefficient suggests linkage. It has been shown that a maximum likelihood method that directly models the sib-pair covariance has more power. This increase in power can also be obtained using the H-E regression procedure by changing the dependent variable from the squared difference to the mean-corrected product of the sibs' trait values. Multiple sibs in a sibship can be accommodated by allowing for the correlations between pairs of products in a generalized least squares procedure. Multiple trait loci, including epistatic interactions, involve only multiple linear regression. Multivariate traits can use the method of Amos et al. [1990] to find the linear function of the traits that maximizes the evidence for linkage, which now leads more simply to a test of significance. Multiple markers can be the basis of a multipoint analysis. Results of simulation studies for a continuous trait are presented that investigate Type I error and power. A similar general scheme can be used to study affected sib pairs, testing whether their identity by descent sharing probabilities are greater than would be expected in the absence of linkage, and to study other types of relative pairs.

Exact transmission-disequilibrium tests with multiallelic markers

The transmission-disequilibrium (TD) test is a powerful method for detecting linkage between marker and disease loci in the presence of linkage disequilibrium. For multiallelic markers, we propose the use of exact tests, which are implemented using both an exact algorithm and Markov chain Monte Carlo simulation. Simulation studies show that exact tests improve both the small sample validity and the power of the TD method. We also compared the usual single-affected-offspring sampling scheme to one in which pairs of affected siblings are sampled. Affected-sib-pair sampling greatly increases the power of the TD method and will be most useful when a sample of affected sib pairs is available from prior linkage studies.

Confidence intervals for relative risk estimates from affected-sib-pair data

Confidence intervals for relative risk parameters estimated using affected-sib-pair data are derived and evaluated for two markers showing previous evidence of linkage to bipolar illness. For D18S41 we found some evidence, and for D18S37 stronger evidence, of relative risks greater than 1, although in both cases the estimated confidence intervals for the parameters are wide.

Model-free age-of-onset methods applied to the linkage of bipolar disorder

We performed Haseman-Elston regression on a set of bipolar pedigrees using each of three dependent variables: a binary trait indicating disease concordance or discordance, a binary trait adjusted for age-of-onset, and the residuals from a survival analysis. The latter two methods, which both adjust for age-of-onset, gave smaller p-values when previous analyses suggested linkage between disease and marker, but not when previous analyses were not suggestive of linkage.

Using family history information to distinguish true and false positive model-free linkage results

Genome scans that test for increased marker identity-by-descent sharing between pairs of affected siblings have become increasingly common. These methods do not specify a priori a genetic model for the disease locus and as such lose the ability to specify the parental source of the disease allele. We propose a method that uses family history information to build a more complete model of disease and marker inheritance, while still avoiding specification of the parameters of the disease model of inheritance. One important use for such a model is to test whether a positive linkage result obtained during the course of a genome scan is a true or false positive result. The key to the new test statistics is the interaction between gender-specific marker identity-by-descent sharing and gender-specific family history of disease. The method is useful when the disease locus of interest has a dominant mode of inheritance and a sufficient number of parents are genotyped at the marker locus. If these conditions are met, the proposed tests have good power to differentiate between true and false positive linkage results.

Decreased expression of striatal signaling genes in a mouse model of Huntington's disease

To understand gene expression changes mediated by a polyglutamine repeat expansion in the human huntingtin protein, we used oligonucleotide DNA arrays to profile approximately 6000 striatal mRNAs in the R6/2 mouse, a transgenic Huntington's disease (HD) model. We found diminished levels of mRNAs encoding components of the neurotransmitter, calcium and retinoid signaling pathways at both early and late symptomatic time points (6 and 12 weeks of age). We observed similar changes in gene expression in another HD mouse model (N171-82Q). These results demonstrate that mutant huntingtin directly or indirectly reduces the expression of a distinct set of genes involved in signaling pathways known to be critical to striatal neuron function.

Correcting for ascertainment bias of relative-risk estimates obtained using affected-sib-pair linkage data

Locus-specific sibling relative risk is often estimated using affected-sib-pair lod score analysis of affected sibships and may be used to decide whether to continue or discontinue the search for additional susceptibility genes. We showed that relative-risk estimates obtained using affected-sib-pair data are asymptotically unbiased when each pair is given a weight inversely proportional to the sibship ascertainment probability. Here we show by simulation that the extent of the bias of relative risks estimated using the incorrect ascertainment weights is small for dominant models, but large for single-locus recessive models and some two-locus heterogeneity models. Since in practice the ascertainment scheme is often unknown, we investigate methods for jointly estimating ascertainment and relative risks from affected-sibship data. Given a sufficient sample size, a reasonable estimate of relative risk may always be obtained using only affected pairs from sibships with two affected and no unaffected siblings. This estimate, which has a large variance, may then be used in a three-stage procedure (which we call the alpha method) to estimate consistently both the ascertainment probabilities and the relative risks with greater precision. We additionally propose correction factors to eliminate small-sample bias of relative risks and investigate the bias due to error in the estimate of disease locus location.

Ascertainment bias in the estimation of sibling genetic risk parameters

The sibling recurrence risk, sibling relative risk, and locus-specific sibling relative risk are fundamental quantities in genetic epidemiologic research and are often estimated without accounting for the sampling scheme. For data generated under some genetic models, bias of estimates may be large if the sampling method is incorrectly modeled. In this paper, we explore the relationship between ascertainment of sibships and estimation and interpretation of genetic risk parameters. In particular, we observe that, although traditional definitions of these population parameters are consistent with each other, implied assumptions about ascertainment and the nature of ascertainment correction differ. In the absence of ascertainment correction, unbiased estimation of sibling recurrence risk and overall sibling relative risk requires single ascertainment, while unbiased estimation of locus-specific sibling relative risk requires complete ascertainment.