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1.  R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping 
Genetics  2014;199(2):359-361.
Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl’s static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data.
doi:10.1534/genetics.114.172742
PMCID: PMC4317647  PMID: 25527287
QTL; data visualization; software; D3
2.  Fourteen Years of R/qtl: Just Barely Sustainable 
R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest release contains 35k lines of R code and 24k lines of C code, plus 15k lines of code for the documentation. Challenges in the development and maintenance of the software are discussed. A key to the success of R/qtl is that it remains a central tool for the chief developer's own research work, and so its maintenance is of selfish importance.
doi:10.5334/jors.at
PMCID: PMC4212690  PMID: 25364504
QTL mapping; software; quantitative trait loci; sustainable software
3.  Quantitative Trait Locus Mapping Methods for Diversity Outbred Mice 
G3: Genes|Genomes|Genetics  2014;4(9):1623-1633.
Genetic mapping studies in the mouse and other model organisms are used to search for genes underlying complex phenotypes. Traditional genetic mapping studies that employ single-generation crosses have poor mapping resolution and limit discovery to loci that are polymorphic between the two parental strains. Multiparent outbreeding populations address these shortcomings by increasing the density of recombination events and introducing allelic variants from multiple founder strains. However, multiparent crosses present new analytical challenges and require specialized software to take full advantage of these benefits. Each animal in an outbreeding population is genetically unique and must be genotyped using a high-density marker set; regression models for mapping must accommodate multiple founder alleles, and complex breeding designs give rise to polygenic covariance among related animals that must be accounted for in mapping analysis. The Diversity Outbred (DO) mice combine the genetic diversity of eight founder strains in a multigenerational breeding design that has been maintained for >16 generations. The large population size and randomized mating ensure the long-term genetic stability of this population. We present a complete analytical pipeline for genetic mapping in DO mice, including algorithms for probabilistic reconstruction of founder haplotypes from genotyping array intensity data, and mapping methods that accommodate multiple founder haplotypes and account for relatedness among animals. Power analysis suggests that studies with as few as 200 DO mice can detect loci with large effects, but loci that account for <5% of trait variance may require a sample size of up to 1000 animals. The methods described here are implemented in the freely available R package DOQTL.
doi:10.1534/g3.114.013748
PMCID: PMC4169154  PMID: 25237114
diversity outbred; haplotype reconstruction; quantitative trait locus mapping; Multiparent Advanced Generation Inter-Cross (MAGIC); multiparental populations; MPP
4.  FMR1 CGG Expansions: Prevalence and Sex Ratios 
We have estimated the prevalence of FMR1 premutation and gray zone CGG repeat expansions in a population-based sample of 19,996 male and female adults in Wisconsin and compared the observed sex ratios of the prevalence of FMR1 CGG premutation and gray zone expansions to theoretical sex ratios. The female premutation prevalence was 1 in 148 and comparable to past research, but the male premutation prevalence of 1 in 290 is somewhat higher than most previous estimates. The female:male premutation prevalence ratio is in line with the theoretically predicted sex ratio. The prevalence of CGG repeats in the gray zone (45–54 repeats) was 1 in 33 females and 1 in 62 males. The prevalence of the “expanded” gray zone (defined here as 41–54 CGG repeats) was 1 in 14 females and 1 in 22 males, leading to a female:male ratio of 1.62 (95% confidence interval 1.39–1.90). This female:male ratio was significantly lower than the expected ratio of 2.0. We examined results from three previously published FMR1 prevalence studies and found similar female:male ratios for CGG repeats in this “expanded” gray zone range (pooled female:male ratio across all four studies 1.66, 95% confidence interval 1.51–1.82). Further research is needed to understand the apparent excess prevalence of males with CGG repeats in this range.
doi:10.1002/ajmg.b.32176
PMCID: PMC3885228  PMID: 23740716
Fragile X; gray zone; premutation; FMR1
5.  A Simple Regression-Based Method to Map Quantitative Trait Loci Underlying Function-Valued Phenotypes 
Genetics  2014;197(4):1409-1416.
Most statistical methods for quantitative trait loci (QTL) mapping focus on a single phenotype. However, multiple phenotypes are commonly measured, and recent technological advances have greatly simplified the automated acquisition of numerous phenotypes, including function-valued phenotypes, such as growth measured over time. While methods exist for QTL mapping with function-valued phenotypes, they are generally computationally intensive and focus on single-QTL models. We propose two simple, fast methods that maintain high power and precision and are amenable to extensions with multiple-QTL models using a penalized likelihood approach. After identifying multiple QTL by these approaches, we can view the function-valued QTL effects to provide a deeper understanding of the underlying processes. Our methods have been implemented as a package for R, funqtl.
doi:10.1534/genetics.114.166306
PMCID: PMC4125409  PMID: 24931408
QTL; function-valued trait; model selection; growth curves
6.  Variation in Genome-Wide Levels of Meiotic Recombination Is Established at the Onset of Prophase in Mammalian Males 
PLoS Genetics  2014;10(1):e1004125.
Segregation of chromosomes during the first meiotic division relies on crossovers established during prophase. Although crossovers are strictly regulated so that at least one occurs per chromosome, individual variation in crossover levels is not uncommon. In an analysis of different inbred strains of male mice, we identified among-strain variation in the number of foci for the crossover-associated protein MLH1. We report studies of strains with “low” (CAST/EiJ), “medium” (C3H/HeJ), and “high” (C57BL/6J) genome-wide MLH1 values to define factors responsible for this variation. We utilized immunofluorescence to analyze the number and distribution of proteins that function at different stages in the recombination pathway: RAD51 and DMC1, strand invasion proteins acting shortly after double-strand break (DSB) formation, MSH4, part of the complex stabilizing double Holliday junctions, and the Bloom helicase BLM, thought to have anti-crossover activity. For each protein, we identified strain-specific differences that mirrored the results for MLH1; i.e., CAST/EiJ mice had the lowest values, C3H/HeJ mice intermediate values, and C57BL/6J mice the highest values. This indicates that differences in the numbers of DSBs (as identified by RAD51 and DMC1) are translated into differences in the number of crossovers, suggesting that variation in crossover levels is established by the time of DSB formation. However, DSBs per se are unlikely to be the primary determinant, since allelic variation for the DSB-inducing locus Spo11 resulted in differences in the numbers of DSBs but not the number of MLH1 foci. Instead, chromatin conformation appears to be a more important contributor, since analysis of synaptonemal complex length and DNA loop size also identified consistent strain-specific differences; i.e., crossover frequency increased with synaptonemal complex length and was inversely related to chromatin loop size. This indicates a relationship between recombination and chromatin compaction that may develop as DSBs form or earlier during establishment of the meiotic axis.
Author Summary
During prophase of meiosis, homologous chromosomes exchange genetic material, in a process known as crossing-over. Crossovers are thought to be essential for proper separation of chromosomes during meiosis but, surprisingly, most mammalian species exhibit substantial individual variation in the number of crossovers per cell. We investigated the basis for this variation by examining localization patterns of crossover-associated proteins in inbred strains of male mice with differing average numbers of crossovers per spermatocyte. Our results indicate that the strain-specific variation is established early in meiotic prophase, possibly even before the DNA is broken in advance of subsequent exchanges between homologous chromosomes.
doi:10.1371/journal.pgen.1004125
PMCID: PMC3907295  PMID: 24497841
7.  Cytological Studies of Human Meiosis: Sex-Specific Differences in Recombination Originate at, or Prior to, Establishment of Double-Strand Breaks 
PLoS ONE  2013;8(12):e85075.
Meiotic recombination is sexually dimorphic in most mammalian species, including humans, but the basis for the male:female differences remains unclear. In the present study, we used cytological methodology to directly compare recombination levels between human males and females, and to examine possible sex-specific differences in upstream events of double-strand break (DSB) formation and synaptic initiation. Specifically, we utilized the DNA mismatch repair protein MLH1 as a marker of recombination events, the RecA homologue RAD51 as a surrogate for DSBs, and the synaptonemal complex proteins SYCP3 and/or SYCP1 to examine synapsis between homologs. Consistent with linkage studies, genome-wide recombination levels were higher in females than in males, and the placement of exchanges varied between the sexes. Subsequent analyses of DSBs and synaptic initiation sites indicated similar male:female differences, providing strong evidence that sex-specific differences in recombination rates are established at or before the formation of meiotic DSBs. We then asked whether these differences might be linked to variation in the organization of the meiotic axis and/or axis-associated DNA and, indeed, we observed striking male:female differences in synaptonemal complex (SC) length and DNA loop size. Taken together, our observations suggest that sex specific differences in recombination in humans may derive from chromatin differences established prior to the onset of the recombination pathway.
doi:10.1371/journal.pone.0085075
PMCID: PMC3869931  PMID: 24376867
8.  Genetic resistance to diet-induced obesity in chromosome substitution strains of mice 
Discovery of genes that confer resistance to diseases such as diet-induced obesity could have tremendous therapeutic impact. We previously demonstrated that the C57BL/6J-ChrA/J/NaJ panel of chromosome substitution strains (CSSs) is a unique model for studying resistance to diet-induced obesity. In the present study, three replicate CSS surveys showed remarkable consistency, with 13 A/J-derived chromosomes reproducibly conferring resistance to high-fat-diet-induced obesity. Twenty CSS intercrosses, one derived from each of the 19 autosomes and chromosome X, were used to determine the number and location of quantitative trait loci (QTLs) on individual chromosomes and localized six QTLs. However, analyses of mean body weight in intercross progeny versus C57BL/6J provided strong evidence that many QTLs discovered in the CSS surveys eluded detection in these CSS intercrosses. Studies of the temporal effects of these QTLs suggest that obesity resistance was dynamic, with QTLs acting at different ages or after different durations of diet exposure. Thus, these studies provide insight into the genetic architecture of complex traits such as resistance to diet-induced obesity in the C57BL/6J-ChrA/J/NaJ CSSs. Because some of the QTLs detected in the CSS intercrosses were not detected using a traditional C57BL/6J × A/J intercross, our results demonstrate that surveys of CSSs and congenic strains derived from them are useful complementary tools for analyzing complex traits.
doi:10.1007/s00335-010-9247-9
PMCID: PMC3831885  PMID: 20127486
9.  High-Throughput Computer Vision Introduces the Time Axis to a Quantitative Trait Map of a Plant Growth Response 
Genetics  2013;195(3):1077-1086.
Automated image acquisition, a custom analysis algorithm, and a distributed computing resource were used to add time as a third dimension to a quantitative trait locus (QTL) map for plant root gravitropism, a model growth response to an environmental cue. Digital images of Arabidopsis thaliana seedling roots from two independently reared sets of 162 recombinant inbred lines (RILs) and one set of 92 near isogenic lines (NILs) derived from a Cape Verde Islands (Cvi) × Landsberg erecta (Ler) cross were collected automatically every 2 min for 8 hr following induction of gravitropism by 90° reorientation of the sample. High-throughput computing (HTC) was used to measure root tip angle in each of the 1.1 million images acquired and perform statistical regression of tip angle against the genotype at each of the 234 RIL or 102 NIL DNA markers independently at each time point using a standard stepwise procedure. Time-dependent QTL were detected on chromosomes 1, 3, and 4 by this mapping method and by an approach developed to treat the phenotype time course as a function-valued trait. The QTL on chromosome 4 was earliest, appearing at 0.5 hr and remaining significant for 5 hr, while the QTL on chromosome 1 appeared at 3 hr and thereafter remained significant. The Cvi allele generally had a negative effect of 2.6–4.0%. Heritability due to the QTL approached 25%. This study shows how computer vision and statistical genetic analysis by HTC can characterize the developmental timing of genetic architectures.
doi:10.1534/genetics.113.153346
PMCID: PMC3813838  PMID: 23979570
root gravitropism; QTL; natural variation; Arabidopsis
10.  Identification of a Novel Polymorphism in X-Linked Sterol-4-Alpha-Carboxylate 3-Dehydrogenase (Nsdhl) Associated with Reduced High-Density Lipoprotein Cholesterol Levels in I/LnJ Mice 
G3: Genes|Genomes|Genetics  2013;3(10):1819-1825.
Loci controlling plasma lipid concentrations were identified by performing a quantitative trait locus analysis on genotypes from 233 mice from a F2 cross between KK/HlJ and I/LnJ, two strains known to differ in their high-density lipoprotein (HDL) cholesterol levels. When fed a standard diet, HDL cholesterol concentration was affected by two significant loci, the Apoa2 locus on Chromosome (Chr) 1 and a novel locus on Chr X, along with one suggestive locus on Chr 6. Non-HDL concentration also was affected by loci on Chr 1 and X along with a suggestive locus on Chr 3. Additional loci that may be sex-specific were identified for HDL cholesterol on Chr 2, 3, and 4 and for non-HDL cholesterol on Chr 5, 7, and 14. Further investigation into the potential causative gene on Chr X for reduced HDL cholesterol levels revealed a novel, I/LnJ-specific nonsynonymous polymorphism in Nsdhl, which codes for sterol-4-alpha-carboxylate 3-dehydrogenase in the cholesterol synthesis pathway. Although many lipid quantitative trait locus have been reported previously, these data suggest there are additional genes left to be identified that control lipid levels and that can provide new pharmaceutical targets.
doi:10.1534/g3.113.007567
PMCID: PMC3789806  PMID: 23979938
QTL; genomics; HDL cholesterol; Nsdhl
11.  Acute-Phase CD8 T Cell Responses That Select for Escape Variants Are Needed to Control Live Attenuated Simian Immunodeficiency Virus 
Journal of Virology  2013;87(16):9353-9364.
The overall CD8 T cell response to human/simian immunodeficiency virus (HIV/SIV) targets a collection of discrete epitope specificities. Some of these epitope-specific CD8 T cells emerge in the weeks and months following infection and rapidly select for sequence variants, whereas other CD8 T cell responses develop during the chronic infection phase and rarely select for sequence variants. In this study, we tested the hypothesis that acute-phase CD8 T cell responses that do not rapidly select for escape variants are unable to control viral replication in vivo as well as those that do rapidly select for escape variants. We created a derivative of live attenuated SIV (SIVmac239Δnef) in which we ablated five epitopes that elicit early CD8 T cell responses and rapidly accumulate sequence variants in SIVmac239-infected Mauritian cynomolgus macaques (MCMs) that are homozygous for the M3 major histocompatibility complex (MHC) haplotype. This live attenuated SIV variant was called m3KOΔnef. Viremia was significantly higher in M3 homozygous MCMs infected with m3KOΔnef than in either MHC-mismatched MCMs infected with m3KOΔnef or MCMs infected with SIVmac239Δnef. Three CD8 T cell responses, including two that do not rapidly select for escape variants, predominated during early m3KOΔnef infection in the M3 homozygous MCMs, but these animals were unable to control viral replication. These results provide evidence that acute-phase CD8 T cell responses that have the potential to rapidly select for escape variants in the early phase of infection are needed to establish viral control in vivo.
doi:10.1128/JVI.00909-13
PMCID: PMC3754066  PMID: 23785211
12.  Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis 
Molecular ecology  2010;20(3):530-544.
Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line and the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes, and each explained around 5–14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping, the candidate gene CG16700 for cold tolerance colocalizing with a QTL was identified.
doi:10.1111/j.1365-294X.2010.04951.x
PMCID: PMC3668310  PMID: 21199023
cold stress; QTL analysis; selective sweep mapping; thermal adaptation
13.  Scram1 is a modifier of spinal cord resistance for astrocytoma on mouse Chr 5 
Mammalian Genome  2011;23(3-4):277-285.
Tumor location can profoundly affect morbidity and patient prognosis even for the same tumor type. Very little is known about whether tumor location is determined stochastically or whether genetic risk factors can affect where tumors arise within an organ system. We have taken advantage of the Nf1−/+;Trp53−/+cis mouse model of astrocytoma/glioblastoma to map genetic loci affecting whether astrocytomas are found in the spinal cord. We identify a locus on distal Chr 5, termed Scram1 for spinal cord resistance to astrocytoma modifier 1 with a LOD score of 5.0 and a genome-wide significance of P<0.004. Mice heterozygous for C57BL/6JX129S4/SvJae at this locus show less astrocytoma in the spinal cord compared to 129S4/SvJae homozygous mice, although we have shown previously that 129S4/SvJae mice are more resistant to astrocytoma than C57BL/6J. Furthermore, the astrocytomas that are found in the spinal cord of Scram1 heterozygous mice arise in older mice. Because spinal cord astrocytomas are very rare and difficult to treat, better understanding of the genetic factors that govern astrocytoma in the spine may suggest new targets of therapy or prevention.
doi:10.1007/s00335-011-9380-0
PMCID: PMC3299925  PMID: 22160242
astrocytoma; glioma; spinal cord; Nf1; p53
14.  Arlm1 is a male-specific modifier of astrocytoma resistance on mouse Chr 12 
Neuro-Oncology  2012;14(2):160-174.
While many cancers show a sex bias, the genetic basis and molecular mechanisms underlying sex bias are not always clear. Astrocytoma and glioblastoma show male predominance in humans. We have shown previously that glial tumors forming in the Nf1−/+; Trp53−/+cis (NPcis) mouse model also show a sex bias in some genetic contexts. Using cross-species comparisons we have identified candidate male-specific modifiers of astrocytoma/glioblastoma. Linkage analysis of B6X(B6X129)-NPcis mice identifies a modifier of astrocytoma resistance specific to males, named Arlm1, on distal mouse Chr 12. Arlm1 is syntenic to human Chr 7p15, 7p21, 7q36, and 14q32 regions that are altered in human glioblastoma. A subset of these genes shows male-specific correlations to glioblastoma patient survival time and represents strong candidates for the Arlm1 modifier gene. Identification of male-specific modifier genes will lead to a better understanding of the molecular basis of male predominance in astrocytoma and glioblastoma.
doi:10.1093/neuonc/nor206
PMCID: PMC3266387  PMID: 22234937
astrocytoma; glioblastoma; modifier; sex differences
15.  Mapping Quantitative Trait Loci onto a Phylogenetic Tree 
Genetics  2012;192(1):267-279.
Despite advances in genetic mapping of quantitative traits and in phylogenetic comparative approaches, these two perspectives are rarely combined. The joint consideration of multiple crosses among related taxa (whether species or strains) not only allows more precise mapping of the genetic loci (called quantitative trait loci, QTL) that contribute to important quantitative traits, but also offers the opportunity to identify the origin of a QTL allele on the phylogenetic tree that relates the taxa. We describe a formal method for combining multiple crosses to infer the location of a QTL on a tree. We further discuss experimental design issues for such endeavors, such as how many crosses are required and which sets of crosses are best. Finally, we explore the method’s performance in computer simulations, and we illustrate its use through application to a set of four mouse intercrosses among five inbred strains, with data on HDL cholesterol.
doi:10.1534/genetics.112.142448
PMCID: PMC3430541  PMID: 22745229
quantitative trait loci (QTL); phylogenetic tree; evolution; multiple crosses; combining crosses
16.  The Lsktm1 Locus Modulates Lung and Skin Tumorigenesis in the Mouse 
G3: Genes|Genomes|Genetics  2012;2(9):1041-1046.
Alleles derived from skin tumor−resistant Car-R mice provide resistance to both skin and lung tumorigenesis over the susceptibility of the SWR/J strain. In an effort to map tumor modifier loci affecting both tumor types, we carried out a genetic linkage analysis in backcross SWR/J x (SWR/J x Car-R) mice and identified a locus (Lsktm1) on chromosome 1 linked to both skin (LOD score = 3.93) and lung (LOD score = 8.74) tumorigenesis. Two genes, Igfbp5 and Igfbp2, residing in this locus and belonging to the insulin-like growth factor binding protein family were expressed at significantly greater levels in normal lung tissue from cancer-resistant Car-R mice than in cancer-susceptible SWR/J mice. Overexpression of the recombinant Igfbp5 and Igfbp2 genes in two lung cancer cell lines significantly inhibited clonogenicity (P < 0.0001). Collectively, we have identified a single polymorphic locus that affects skin and lung tumorigenesis and identify Igfbp5 and Igfbp2 as candidate modifier genes of lung tumorigenesis.
doi:10.1534/g3.112.003525
PMCID: PMC3429918  PMID: 22973541
disease models; cancer modifier genes; lung cancer; quantitative trait loci (QTLs); skin cancer; single-nucleotide polymorphisms
17.  Ex Vivo SIV-Specific CD8 T Cell Responses in Heterozygous Animals Are Primarily Directed against Peptides Presented by a Single MHC Haplotype 
PLoS ONE  2012;7(8):e43690.
The presence of certain MHC class I alleles is correlated with remarkable control of HIV and SIV, indicating that specific CD8 T cell responses can effectively reduce viral replication. It remains unclear whether epitopic breadth is an important feature of this control. Previous studies have suggested that individuals heterozygous at the MHC class I loci survive longer and/or progress more slowly than those who are homozygous at these loci, perhaps due to increased breadth of the CD8 T cell response. We used Mauritian cynomolgus macaques with defined MHC haplotypes and viral inhibition assays to directly compare CD8 T cell efficacy in MHC-heterozygous and homozygous individuals. Surprisingly, we found that cells from heterozygotes suppress viral replication most effectively on target cells from animals homozygous for only one of two potential haplotypes. The same heterozygous effector cells did not effectively inhibit viral replication as effectively on the target cells homozygous for the other haplotype. These results indicate that the greater potential breadth of CD8 T cell responses present in heterozygous animals does not necessarily lead to greater antiviral efficacy and suggest that SIV-specific CD8 T cell responses in heterozygous animals have a skewed focus toward epitopes restricted by a single haplotype.
doi:10.1371/journal.pone.0043690
PMCID: PMC3425510  PMID: 22928016
18.  Quantile-Based Permutation Thresholds for Quantitative Trait Loci Hotspots 
Genetics  2012;191(4):1355-1365.
Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume “omic” data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.
doi:10.1534/genetics.112.139451
PMCID: PMC3416013  PMID: 22661325
hotspots; permutation tests; multiple traits; LOD scores; quantitative trait loci (QTL)
19.  xQTL workbench: a scalable web environment for multi-level QTL analysis 
Bioinformatics  2012;28(7):1042-1044.
Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator.
Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org.
Contact: m.a.swertz@rug.nl
doi:10.1093/bioinformatics/bts049
PMCID: PMC3315722  PMID: 22308096
20.  Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines 
Genetics  2012;190(2):403-412.
The mouse Collaborative Cross (CC) is a panel of eight-way recombinant inbred lines: eight diverse parental strains are intermated, followed by repeated sibling mating, many times in parallel, to create a new set of inbred lines whose genomes are random mosaics of the genomes of the original eight strains. Many generations are required to reach inbreeding, and so a number of investigators have sought to make use of phenotype and genotype data on mice from intermediate generations during the formation of the CC lines (so-called pre-CC mice). The development of a hidden Markov model for genotype reconstruction in such pre-CC mice, on the basis of incompletely informative genetic markers (such as single-nucleotide polymorphisms), formally requires the two-locus genotype probabilities at an arbitrary generation along the path to inbreeding. In this article, I describe my efforts to calculate such probabilities. While closed-form solutions for the two-locus genotype probabilities could not be derived, I provide a prescription for calculating such probabilities numerically. In addition, I present a number of useful quantities, including single-locus genotype probabilities, two-locus haplotype probabilities, and the fixation probability and map expansion at each generation along the course to inbreeding.
doi:10.1534/genetics.111.132647
PMCID: PMC3276635  PMID: 22345609
21.  Haplotype Probabilities in Advanced Intercross Populations 
G3: Genes|Genomes|Genetics  2012;2(2):199-202.
Advanced intercross populations, in which multiple inbred strains are mated at random for many generations, have the advantage of greater precision of genetic mapping because of the accumulation of recombination events across the multiple generations. Related designs include heterogeneous stock and the diversity outcross population. In this article, I derive the two-locus haplotype probabilities on the autosome and X chromosome with these designs. These haplotype probabilities provide the key quantities for developing hidden Markov models for the treatment of missing genotype information. I further derive the map expansion in these populations, which is the frequency of recombination breakpoints on a random chromosome.
doi:10.1534/g3.111.001818
PMCID: PMC3284327  PMID: 22384398
advanced intercross lines; heterogeneous stock; diversity outcross; map expansion; Collaborative Cross; Mouse Genetic Resource
22.  R/qtl: high-throughput multiple QTL mapping 
Bioinformatics  2010;26(23):2990-2992.
Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.
Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.
Contact: kbroman@biostat.wisc.edu
doi:10.1093/bioinformatics/btq565
PMCID: PMC2982156  PMID: 20966004
23.  Cross-Reactive T Cells Are Involved in Rapid Clearance of 2009 Pandemic H1N1 Influenza Virus in Nonhuman Primates 
PLoS Pathogens  2011;7(11):e1002381.
In mouse models of influenza, T cells can confer broad protection against multiple viral subtypes when antibodies raised against a single subtype fail to do so. However, the role of T cells in protecting humans against influenza remains unclear. Here we employ a translational nonhuman primate model to show that cross-reactive T cell responses play an important role in early clearance of infection with 2009 pandemic H1N1 influenza virus (H1N1pdm). To “prime” cellular immunity, we first infected 5 rhesus macaques with a seasonal human H1N1 isolate. These animals made detectable cellular and antibody responses against the seasonal H1N1 isolate but had no neutralizing antibodies against H1N1pdm. Four months later, we challenged the 5 “primed” animals and 7 naive controls with H1N1pdm. In naive animals, CD8+ T cells with an activated phenotype (Ki-67+ CD38+) appeared in blood and lung 5–7 days post inoculation (p.i.) with H1N1pdm and reached peak magnitude 7–10 days p.i. In contrast, activated T cells were recruited to the lung as early as 2 days p.i. in “primed” animals, and reached peak frequencies in blood and lung 4–7 days p.i. Interferon (IFN)-γ Elispot and intracellular cytokine staining assays showed that the virus-specific response peaked earlier and reached a higher magnitude in “primed” animals than in naive animals. This response involved both CD4+ and CD8+ T cells. Strikingly, “primed” animals cleared H1N1pdm infection significantly earlier from the upper and lower respiratory tract than the naive animals did, and before the appearance of H1N1pdm-specific neutralizing antibodies. Together, our results suggest that cross-reactive T cell responses can mediate early clearance of an antigenically novel influenza virus in primates. Vaccines capable of inducing such cross-reactive T cells may help protect humans against severe disease caused by newly emerging pandemic influenza viruses.
Author Summary
Antibodies against influenza target the highly mutable proteins on the virus surface. Influenza pandemics are caused by novel viruses whose surface proteins are so different from previously circulating viruses as to be unrecognizable by most individuals' antibodies. We hypothesized that T cells might be capable of reducing the severity of infection with pandemic influenza viruses, against which antibodies are ineffective. Experiments in mice have supported this idea, but the ability of T cells to protect humans against influenza has remained unclear. We therefore tested our hypothesis in macaque monkeys, whose physiology and immune systems closely resemble those of humans. We used a seasonal virus to “prime” macaques to make immune responses against influenza and found that these animals were able to control infection with 2009 H1N1 pandemic influenza viruses more effectively than animals that had not been “primed.” Protection was associated with T cell responses, but not antibodies, that were quickly “recalled” after challenge with the pandemic virus. Our results suggest that “cross-reactive” T cells could play an important role in controlling influenza in humans. Vaccines designed to induce strong T cell responses in addition to antibodies could offer enhanced protection against emerging influenza viruses.
doi:10.1371/journal.ppat.1002381
PMCID: PMC3213121  PMID: 22102819
24.  An SNP-Based Linkage Map for Zebrafish Reveals Sex Determination Loci 
G3 (Bethesda, Md.)  2011;1(1):3-9.
A surprising diversity of mechanisms controls sex determination of vertebrate organisms, even among closely related species. Both genetic and temperature-dependent systems of sex determination have been described in teleost fish. In the common zebrafish model organism, heteromorphic sex chromosomes are not observed, and the potential role of a genetic component of sex determination remains largely unknown. Here we report a genome-wide linkage study of sex determination in zebrafish using a novel SNP genetic map. We identified loci on zebrafish chromosomes 5 (LOD score 7.9) and 16 (LOD score 9.3) governing sex determination as a complex trait, rather than as an XY or ZW genetic system. Each of these loci contains a prominent candidate gene with a conserved role in sex determination across additional species that suggest potential mechanisms of sex determination in zebrafish. The chromosome 5 locus harbors dmrt1, a key gene in sex determination from fruit flies to humans; mutation of the human DMRT1 ortholog is a cause of complete sex reversal of XY individuals. The chromosome 16 locus harbors cyp21a2; mutation of the human CYP21A2 ortholog is one of the more common causes of pseudohermaphroditism. Mutation detection at each of these candidate genes within the zebrafish cross identified hypomorphic variants on the female-associated allele of each locus. The two loci together accounted for 16% of variance of the trait. Interacting environmental cues are likely to be an additional important component of sex determination in zebrafish.
doi:10.1534/g3.111.000190
PMCID: PMC3178105  PMID: 21949597
DMRT1; doublesex; CYP21A2; 21-hydroxylase; sex determination; teleost fish; SNP; genetic map; recombination rate; genetic diversity; structure; zebrafish
25.  Differential MHC class I expression in distinct leukocyte subsets 
BMC Immunology  2011;12:39.
Background
MHC class I proteins are partly responsible for shaping the magnitude and focus of the adaptive cellular immune response. In humans, conventional wisdom suggests that the HLA-A, -B, and -C alleles are equally expressed on the majority of cell types. While we currently have a thorough understanding of how total MHC class I expression varies in different tissues, it has been difficult to examine expression of single MHC class I alleles due to the homogeneity of MHC class I sequences. It is unclear how cDNA species are expressed in distinct cell subsets in humans and particularly in macaques which transcribe upwards of 20 distinct MHC class I alleles at variable levels.
Results
We examined MHC gene expression in human and macaque leukocyte subsets. In humans, while we detected overall differences in locus transcription, we found that transcription of MHC class I genes was consistent across the leukocyte subsets we studied with only small differences detected. In contrast, transcription of certain MHC cDNA species in macaques varied dramatically by up to 45% between different subsets. Although the Mafa-B*134:02 RNA is virtually undetectable in CD4+ T cells, it represents over 45% of class I transcripts in CD14+ monocytes. We observed parallel MHC transcription differences in rhesus macaques. Finally, we analyzed expression of select MHC proteins at the cell surface using fluorescent peptides. This technique confirmed results from the transcriptional analysis and demonstrated that other MHC proteins, known to restrict SIV-specific responses, are also differentially expressed among distinct leukocyte subsets.
Conclusions
We assessed MHC class I transcription and expression in human and macaque leukocyte subsets. Until now, it has been difficult to examine MHC class I allele expression due to the similarity of MHC class I sequences. Using two novel techniques we showed that expression varies among distinct leukocyte subsets of macaques but does not vary dramatically in the human cell subsets we examined. These findings suggest pathogen tropism may have a profound impact on the shape and focus of the MHC class I restricted CD8+ T cell response in macaques.
doi:10.1186/1471-2172-12-39
PMCID: PMC3155488  PMID: 21762519

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