Correcting Coalescent Analyses for Panel-Based SNP Ascertainment

Single-nucleotide polymorphism (SNP) data are routinely obtained by sequencing a region of interest in a small panel, constructing a chip with probes specific to sites found to vary in the panel, and using the chip to assay subsequent samples. The size of the chip is often reduced by removing low-frequency alleles from the set of SNPs. Using coalescent estimation of the scaled population size parameter, Θ, as a test case, we demonstrate the loss of information inherent in this procedure and develop corrections for coalescent analysis of SNPs obtained via a panel. We show that more accurate Θ-estimates can be recovered if the panel size is known, but at considerable computational cost as the panel individuals must be explicitly modeled in the analysis. We extend this technique to apply to the case where rare alleles have been omitted from the SNP panel. We find that when appropriate corrections for panel ascertainment and rare-allele omission are used, the biases introduced by ascertainment are largely correctable, but recovered estimates are less accurate than would be obtained with fully sequenced data. This method is then applied to recombinant multiple population data to investigate the effects of recombination and migration on the estimate of Θ.     

Center for the evaluation of risks to human reproduction--the first five years

The National Toxicology Program (NTP) Center for the Evaluation of Risks to Human Reproduction (NTP-CERHR) was established by the NTP and the National Institute of Environmental Health Sciences (NIEHS) in 1998 to address the impact of chemical exposures on human reproductive and developmental health and to serve as an environmental and reproductive health resource for government agencies and the general public. The purpose of this report is to provide an overview of the Center activities and a summary of NTP conclusions on chemicals evaluated during this time period. CERHR evaluations involve the critical review of reproductive, developmental, and other relevant toxicity data by independent panels of scientists. The products of these evaluations are expert panel reports. The public has opportunities to provide oral comments at the panel meeting and written comments on draft and final expert panel reports. The NTP evaluates these comments, the conclusions of the expert panel, and any new data not available at the time of the panel meeting, and prepares an NTP brief that describes in plain language the NTP's conclusions on the reproductive and developmental hazard from specified chemical exposures. The NTP brief, expert panel report, and public comments comprise the NTP monograph on the chemical. Monographs are sent to federal regulatory agencies, the NTP Executive Committee, and the NTP Board of Scientific Counselors, and are publicly available. Over the last five years, CERHR conducted expert panel evaluations on 14 chemicals. At this time, 13 panel reports have been published and 12 NTP-CERHR monographs have been issued. Additionally, CERHR conducted a 2-day workshop on the role of thyroid hormones in reproductive and developmental health.     

Construction and optimization of a dog whole-genome radiation hybrid panel

A dog whole-genome radiation hybrid (WGRH) panel including 126 clones was constructed by fusing dog fibroblasts irradiated at 5000 rads with thymidine kinase-deficient hamster cells. The average retention frequency of the panel designated as RHDF5000 is 21%, and its resolution power is estimated at 600 kb. The data provided by typing 400 markers were used to estimate linkage power changes subsequent to panel reduction. These changes were analyzed by recomputing typing data from five reduced panels. From these simulations, the parameters allowing investigation of the evolution of the linkage power in the course of panel reduction were determined. Guidelines for constructing a WGRH panel are proposed. Received: 23 February 1999 / Accepted: 11 May 1999     

Life Cycle Assessment of Novel Aircraft Interior Panels Made from Renewable or Recyclable Polymers with Natural Fiber Reinforcements and Non‐Halogenated Flame Retardants

A comprehensive life cycle assessment of panels for aircraft interiors was conducted, including both a conventional glass fiber‐reinforced panel and different novel sustainable panels. The conventional panel is made of a glass fiber‐reinforced thermoset composite with halogenated flame retardant, whereas the sustainable panels are made of renewable or recyclable polymers, natural fiber reinforcements, and nonhalogenated flame retardants. Four different sustainable panels were investigated: a geopolymer‐based panel; a linseed‐oil–based biopolymer panel; and two thermoplastic panels, one with polypropylene (PP) and another with polylactic acid (PLA). All of the sustainable panels were developed to fulfil fire resistance requirements and to be lighter than the conventional panels in order to reduce fuel consumption and air pollutant emissions from the aircraft. The environmental impacts associated with energy consumption and air emissions were assessed, as well as other environmental impacts resulting from the extraction and processing of materials, transportation of materials and waste, panel manufacturing, use, maintenance, and end of life (EoL). All the sustainable panels showed better environmental performance than the conventional panel. The overall impacts of the sustainable panels were offset by the environmental benefits in the use stage attributed to weight reduction. One square meter of the novel panels could save to 6,000 kilograms of carbon dioxide equivalents. The break‐even point (in months) at which the use of sustainable panels would yield an environmental benefit relative to the impacts arising in production and EoL was as follows: 1.2 for the geopolymer panel; 1.7 for the biopolymer panel; 10.4 for the PLA panel; and 54.5 for the PP panel.     

Comparison of genotype imputation strategies using a combined reference panel for chicken population

Using whole-genome sequence (WGS) data are supposed to be optimal for genome-wide association studies and genomic predictions. However, sequencing thousands of individuals of interest is expensive. Imputation from single nucleotide polymorphisms panels to WGS data is an attractive approach to obtain highly reliable WGS data at low cost. Here, we conducted a genotype imputation study with a combined reference panel in yellow-feather dwarf broiler population. The combined reference panel was assembled by sequencing 24 key individuals of a yellow-feather dwarf broiler population (internal reference panel) and WGS data from 311 chickens in public databases (external reference panel). Three scenarios were investigated to determine how different factors affect the accuracy of imputation from 600 K array data to WGS data, including: genotype imputation with internal, external and combined reference panels; the number of internal reference individuals in the combined reference panel; and different reference sizes and selection strategies of an external reference panel. Results showed that imputation accuracy from 600 K to WGS data were 0.834±0.012, 0.920±0.007 and 0.982±0.003 for the internal, external and combined reference panels, respectively. Increasing the reference size from 50 to 250 improved the accuracy of genotype imputation from 0.848 to 0.974 for the combined reference panel and from 0.647 to 0.917 for the external reference panel. The selection strategies for the external reference panel had no impact on the accuracy of imputation using the combined reference panel. However, if only an external reference panel with reference size >50 was used, the selection strategy of minimizing the average distance to the closest leaf had the greatest imputation accuracy compared with other methods. Generally, using a combined reference panel provided greater imputation accuracy, especially for low-frequency variants. In conclusion, the optimal imputation strategy with a combined reference panel should comprehensively consider genetic diversity of the study population, availability and properties of external reference panels, sequencing and computing costs, and frequency of imputed variants. This work sheds light on how to design and execute genotype imputation with a combined external reference panel in a livestock population.     

Characterisation of a bovine/murine hybrid cell panel informative for all bovine autosomes

A bovine/murine hybrid cell panel consisting of 57 cell lines was typed with 124 markers by PCR, Southern hybridisation and isozyme analysis in order to establish its utility as a resource for genome mapping. All bovine chromosomes, including the sex chromosomes were represented in the panel. Computerised analysis of syntenies indicated that there are no cell lines containing only a single bovine chromosome. The panel was used to map 10 new bovine microsatellite markers, and the MYL6 and CPE genes. This panel is informative for all bovine chromosomes other than the sex-specific region of the X chromosome and can be used in synteny mapping studies. At present, due to the relatively small number of markers typed, the resolution of the panel does not go beyond the chromosomal level.     

MODELING THE EVOLUTION OF THE PERFORMANCE OF A SENSORY PANEL: A MIXED-MODEL AND CONTROL CHART APPROACH

A sensory panel is often used to profile the same type of product with the same set of attributes for many years. We are interested in characterizing the evolution of the performance of such a panel (and its panelists) over time. This article presents a methodology based on a mixed‐model approach that takes into account the evolution of both panel and panelist in the same model. At the panel level, linear and quadratic evolutions of the performance are tested. At the panelist level, the method allows detection of whether some panelists perform better than others, and whether this difference remains the same or evolves over time. This mixed‐model approach is followed by a graphical representation using a control chart method to identify occasional outliers. Data used to illustrate this methodology are eight sensory profiling data sets collected on ready‐made frozen meals between 1997 and 2001 (every 6 months). The performance index chosen as an example in this study is the individual repeatability measured by standard deviation over replicates.     

Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil

Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.     

人巨细胞病毒IgM抗体国家参考品的研制

目的为了对人巨细胞病毒(Human cytomegalovirus,HCMV)IgM抗体检测试剂进行统一评价,研制HCMVIgM抗体国家参考品,用于控制试剂盒的质量。方法收集正常人与感染者的标本,采用多实验室联合标定的方法确认参考品的试验结果,并经一系列的破坏条件进行稳定性和均匀性考核。结果考核的敏感性和准确性符合国家参考品的要求。结论该参考品能用于临床检测试剂的质量控制。     

Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry

Human genetic markers linked with the X chromosome (X-linked) are used in the field of population and medical genetics, as well as for DNA identification of individuals in forensic science and forensic medicine. We proposed an XSNPid panel that consists of 66 unlinked single nucleotide X chromosome markers and developed a protocol for their multiplex genotyping using multilocus PCR and MALDI-TOF mass spectrometry. The XSNPid panel is genotyped within two multiplexes (36 and 30 markers). The developed protocol provides an efficient genotype reading; the fraction of determined genotypes is 98.29%. The high level of gene diversity (0.461) for the X-linked SNPs included in the panel is characteristic of the Russian population. A total of 63 out of 66 markers that provide a high efficiency of genotyping and independent inheritance are suitable for DNA identification purposes. The XSNPid panel is characterized by a very high discriminating ability when studying the Russian population. The probability of genotype coincidence in two unrelated individuals is 9 × 10^–27 for women and 2 × 10^–18 for men. Also, the XSNPid panel has a greater multiplex capacity in addition to a higher discriminating ability compared to the other closest analogues of the X chromosome SNP sets, which makes it more cost effective and less time consuming. The XSNPid panel is a convenient tool, not only for individual DNA identification, but also for population genetic studies.     

The use of diversity profiling to characterize chemical modulators of the histone deacetylases

Target specificity and off-target liabilities are routinely monitored during the early phases of drug discovery for most kinase projects. Typically these criteria are evaluated using a profiling panel comprised of a diverse collection of in vitro kinase assays and relates compound structure to potency and selectivity. The success of these efforts has led to the design of similar panels for phosphatase, protease, and epigenetic targets. Here the implementation of an epigenetic profiling panel, comprised of eleven histone deacetylases (HDACs) and one histone acetyltransferase (HAT), was used to evaluate chemical modulators of these enzymes. HDAC inhibitors (HDACi) such as sodium butyrate and trichostatin A demonstrate diverse biological effects which have led to broad speculation about their therapeutic potential in multiple disease states. Some HDACi have demonstrated tumor suppression in vivo and recently Zolinza was the first HDACi approved by the FDA for the treatment of cutaneous T-cell lymphoma. While HDACi have demonstrated therapeutic utility, many of the first generation compounds are pan-inhibitors. Thus, use of an HDAC profiling panel will be essential in achieving isoform specificity of the next generation of inhibitors. To this end, twenty-one compounds, twelve of which are known to have activities against the HDACs, were tested to evaluate the utility of the epigenetic panel. Additionally, these compounds were tested against a larger 72 member enzyme panel comprised of kinase, phosphatase and protease activities. This effort represents the first time these compounds have been profiled with such a broad range of biochemical activities.     

Construction of a Panel of Transgenic Mice Containing a Contiguous 2-Mb Set of YAC/P1 Clones from Human Chromosome 21q22.2

Libraries of the entire human genome, or regions of the genome, have been made in bacteria, yeast, and somatic cells. We have expanded this strategy using overlapping YACs and P1s from human 21q22.2 (the Down syndrome region) to create a panel of transgenic mice containing DNA that encompasses this region of the human genome. Together the members of the in vivo library, each with a unique transgene (four YACs and four P1s), contain approximately 2 Mb of contiguous DNA. The integrity, stable inheritance, and expression of a coding sequence for each member of the YAC panel are demonstrated, and the uses of the panel are described.     

Killer cell immunoglobulin-like receptor (KIR) gene content variation in the HGDP-CEPH populations

In the present study, we investigate patterns of variation in the KIR cluster in a large and well-characterized sample of worldwide human populations in the Human Genome Diversity Project-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) panel in order to better understand the patterns of diversity in the region. Comparison of KIR data with that from other genomic regions allows control for strictly demographic factors; over 500,000 additional genomic markers have been typed in this panel by other investigators and the data made publicly available. Presence/absence frequencies and haplotypic associations for the KIR region are analyzed in the 52 populations comprising the panel and in accordance with major world regions (Africa, Middle East, Central Asia, East Asia, Europe, Americas, and Oceania). These data represent the first overview of KIR population genetics in the well-documented HGDP-CEPH panel and suggest different evolutionary histories and recent selection in the KIR gene cluster.     

A high-resolution molecular-based panel of assays for identification and characterization of human embryonic stem cell lines

Meticulous characterization of human embryonic stem cells (hESC) is critical to their eventual use in cell-based therapies, particularly in view of the diverse methods for derivation and maintenance of these cell lines. However, characterization methods are generally not standardized and many currently used assays are subjective, making dependable and direct comparison of cell lines difficult. In order to address this problem, we selected 10 molecular-based high-resolution assays as components of a panel for characterization of hESC. The selection of the assays was primarily based on their quantitative or objective (rather than subjective) nature. We demonstrate the efficacy of this panel by characterizing 4 hESC lines, derived in two different laboratories using different derivation techniques, as pathogen free, genetically stable, and able to differentiate into derivatives of all three germ layers. Our panel expands and refines a characterization panel previously proposed by the International Stem Cell Initiative and is another step toward standardized hESC characterization and quality control, a crucial element of successful hESC research and clinical translation.     

EVALUATION OF WINE QUALITY USING A SMALL-PANEL HEDONIC SCALING METHOD

A hedonic scoring method for evaluating wines with a small panel was examined for reliability, effects of training level and agreement with a traditional 20-point scoring technique. The method was found to differentiate among qualities of 14 domestic Sauvignon Blanc wines with good reliability. Four panels were tested, three with a high degree of experience in wine judging and a fourth consisting of fine wine consumers with no special training. The three experienced panels agreed well about the wines' quality scores. Mean panel scores were less highly correlated (although still positive) with the untrained panel, which showed higher variability and lower reliability. Mean scores from the hedonic method were correlated at r =+0.94 with mean scores from a 20-point quality judging procedure. The small panel hedonic method is suitable for generating quality scores for consumer guidance in large scale wine surveys, as are commonly found in popular wine periodicals.     

Demographic and Psychological Predictors of Panel Attrition: Evidence from the New Zealand Attitudes and Values Study

This study examines attrition rates over the first four years of the New Zealand Attitudes and Values Study, a longitudinal national panel sample of New Zealand adults. We report the base rate and covariates for the following four distinct classes of respondents: explicit withdrawals, lost respondents, intermittent respondents and constant respondents. A multinomial logistic regression examined an extensive range of demographic and socio-psychological covariates (among them the Big-Six personality traits) associated with membership in these classes (N = 5,814). Results indicated that men, Māori and Asian peoples were less likely to be constant respondents. Conscientiousness and Honesty-Humility were also positively associated with membership in the constant respondent class. Notably, the effect sizes for the socio-psychological covariates of panel attrition tended to match or exceed those of standard demographic covariates. This investigation broadens the focus of research on panel attrition beyond demographics by including a comprehensive set of socio-psychological covariates. Our findings show that core psychological covariates convey important information about panel attrition, and are practically important to the management of longitudinal panel samples like the New Zealand Attitudes and Values Study.     

Genomic selection using low density marker panels with application to a sire line in pigs

Background

Genomic selection has become a standard tool in dairy cattle breeding. However, for other animal species, implementation of this technology is hindered by the high cost of genotyping. One way to reduce the routine costs is to genotype selection candidates with an SNP (single nucleotide polymorphism) panel of reduced density. This strategy is investigated in the present paper. Methods are proposed for the approximation of SNP positions, for selection of SNPs to be included in the low-density panel, for genotype imputation, and for the estimation of the accuracy of genomic breeding values. The imputation method was developed for a situation in which selection candidates are genotyped with an SNP panel of reduced density but have high-density genotyped sires. The dams of selection candidates are not genotyped. The methods were applied to a sire line pig population with 895 German Piétrain boars genotyped with the PorcineSNP60 BeadChip.

Results

Genotype imputation error rates were 0.133 for a 384 marker panel, 0.079 for a 768 marker panel, and 0.022 for a 3000 marker panel. Error rates for markers with approximated positions were slightly larger. Availability of high-density genotypes for close relatives of the selection candidates reduced the imputation error rate. The estimated decrease in the accuracy of genomic breeding values due to imputation errors was 3% for the 384 marker panel and negligible for larger panels, provided that at least one parent of the selection candidates was genotyped at high-density.Genomic breeding values predicted from deregressed breeding values with low reliabilities were more strongly correlated with the estimated BLUP breeding values than with the true breeding values. This was not the case when a shortened pedigree was used to predict BLUP breeding values, in which the parents of the individuals genotyped at high-density were considered unknown.

Conclusions

Genomic selection with imputation from very low- to high-density marker panels is a promising strategy for the implementation of genomic selection at acceptable costs. A panel size of 384 markers can be recommended for selection candidates of a pig breeding program if at least one parent is genotyped at high-density, but this appears to be the lower bound.