Principal component analysis of gene frequencies of Chinese populations

Principal components (PCs) were calculated based on gene frequencies of 130 alleles at 38 loci in Chinese populations, and geographic PC maps were constructed. The first PC map of the Han shows the genetic difference between Southern and Northern Mongoloids, while the second PC indicates the gene flow between Caucasoid and Mongoloids. The first PC map of the Chinese ethnic minorities is similar to that of the second PC map of the Han, while their second PC map is similar to the first PC map of the Han. When calculating PC with the gene frequency data from both the Han and ethnic minorities, the first and second PC maps most resemble those of the ethnic minorities alone. The third and fourth PC maps of Chinese populations may reflect historical events that allowed the expansion of the populations in the highly civilized regions. A clear-cut boundary between Southern and Northern Mongoloids in the synthetic map of the Chinese populations was observed in the zone of the Yangtze River. We suggest that the a     

GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database(GGVD). GGVD hosts a total of ～41.44 million SNPs, ～5.14 million indels, 6,193 selected loci, and 112 introgression regions. Users can freely visualize the frequency of genomic variations in geographical maps,selective sweeps in interactive tables, Manhattan plots, or line charts, as well as the heatmap patterns of the SNP genotype. Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early, middle, and late stages. For facilitating access to sequence features, the UCSC Genome Browser, BLAT, BLAST, Lift Over, and pcadapt are also integrated into GGVD.GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs, and it is publicly available at http://animal.nwsuaf.edu.cn/Goat Var.     

Genetic Mapping of Laminaria japonica and L. Iongissima Using Amplified Fragment Length Polymorphism Markers in a ＂Two-Way Pseudo- Testcross＂ Strategy

With a ＂two-way pseudo-testcross＂ mapping strategy, we applied the amplified fragment length polymorphism （AFLP） markers to construct two moderate density genetic linkage maps for Laminaria. The linkage maps were generated from the 60 progenies of the F1 cross family （Laminaria iongissima Aresch. × L. Japonica Miyabe） with twenty pairs of primer combinations. Of the 333 polymorphic loci scored in 60 progenies, 173 segregated in a 1：1 ratio, corresponding to DNA polymorphisms heterozygous in a single parent, and the other 58 loci existing in both parents followed a 3：1 Mendelian segregation ratio. Among the loci with 1：1 segregating ratios, 79 loci were ordered in 14 linkage groups （648.6 cM） of the paternal map, and 72 loci were ordered in 14 linkage groups （601.9 cM） of the maternal map. The average density of loci was approximately 1 per 8 cM. To Investigate the homologies between two parental maps, we used 58 loci segregated 3：1 for further analysis, and deduced one homologous linkage group. The linkage data developed in these maps will be useful for detecting loci-controlling commercially important traits for Laminaria.     

BIGpre: a quality assessment package for next-generation sequencing data

The emergence of next-generation sequencing (NGS) technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Although there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn’t taken into account the sequencing errors when dealing with the duplicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://bigpre.sourceforge.net/.     

EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test

In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon–Mann–Whitney(WMW) test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calculate the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we presented different optimization strategies and developed a parallel solution. Using our program,the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molecular biomarkers for lung carcinoma and chronic obstructive pulmonary disease(COPD). We foundthat approximated P values were generally higher than the exact solution provided by EDISONWMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http://www.ccb.uni-saarland.de/software/wtest/.     

METHODS FOR DETECTION AND ESTIMATION OF LINKAGE BETWEEN A MARKER LOCUS AND QUANTITATIVE TRAIT LOCI Ⅰ. USING F_2 FAMILY SUBPOPULATION

Several methods heve been proposed over the years to detect linkage between a marker gene and a quantitative trait locus (QTL). Use of isozymes and restriction fragment length polymorphisms (RFLPs) as genetic markers has encouraged the development of new methods to detect linkage. In the paper authors present three methods to detect linkage and two methods to measure recombination frequency (r). The three methods that detect linkage are fit for the test of one or several QTLs of quantitative trait considered as long as the net gene effect vaIue of all loci belonging to a linkage cluster is greater significantly than zero, irrespective of their linkage relationship among the several QTLs.     

A Preliminary Study of the Noninvasive Remote Control System for Rat Bio-Robot

<正> A system is described here that can noninvasively control the navigation of freely behaving rat via ultrasonic,epidermaland LED photic stimulators on the back.The system receives commands from a remote host computer to deliver specifiedelectrical stimulations to the hearing,pain and visual senses of the rat respectively.The results demonstrate that the three stimuliwork in groups for the rat navigation.We can control the rat to proceed and make right and left turns with great efficiency.Thisexperiment verified that the rat was able to reach a setting destination in the way of cable with the help of a person through theappropriate coordination of the three stimulators.The telemetry video camera mounted on the head of the rat also achieveddistant image acquisition and helped to adjust its navigation path over a distance of 300 m.In a word,the non-invasive motioncontrol navigation system is a good,stable and reliable bio-robot.     

两个基因座位的遗传平衡原理

由于许多教科书中关于连锁平衡的介绍,多是引用结论或是推导不太严谨,使学生在学习群体遗传学时对理解连锁平衡的原理感到困难。本文从遗传平衡的基本条件出发,通过较严谨的数学推导,介绍了两个基因座的连锁平衡条件、平衡过程等原理,供教师和学生在群体遗传学教学中参考。Abstract: Because linkage equilibrium is introduced by directly quoting the conclusions or imprecise mathematical reasoning in most of textbooks, many students are puzzled with the problem of linkage equilibrium when they learn population genetics. Based on the radical conditions of genetic equilibrium, the principle of linkage equilibrium condition and process, for two gene loci is introduced by precise mathematical reasoning. The article may provide reference to teachers and students in the teaching and learning of population genetics.     

Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis

SUMMARY: The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. AVAILABILITY: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. SUPPLEMENTARY INFORMATION: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.     

MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

With the advent of RFLPs, genetic linkage maps are now being assembled for a number of organisms including both inbred experimental populations such as maize and outbred natural populations such as humans. Accurate construction of such genetic maps requires multipoint linkage analysis of particular types of pedigrees. We describe here a computer package, called MAPMAKER, designed specifically for this purpose. The program uses an efficient algorithm that allows simultaneous multipoint analysis of any number of loci. MAPMAKER also includes an interactive command language that makes it easy for a geneticist to explore linkage data. MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used.     

三点自交法和两点最大似然法构建水稻F2群体分子标记连锁图谱的比较

根据连锁遗传的原理,列出了三点自交法和两点自交最大似然(ML)法估算显性标记遗传距离的具体步骤和算法,将水稻F2群体含香味基因Aro及其连锁的RFLP数据转变为显性标记数据后,用上述两种方法构建的连锁图谱与用MAPMAKER软件计算共显性数据得到的图谱排序相同、标记间距离相近．但是标记数据存在较大程度偏分离时,由三点自交法构建的图谱中标记间图距有增大趋势．作者为提高作图精确性,简化计算过程,讨论了三点自交法对估算重组值的影响及其在分子标记作图中的应用价值,并建议将共显性标记转变为显性标记时进行两次自交ML法估算。     

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control

rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps. AVAILABILITY: rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm     

A genetic map of chromosome 1: comparison of different data sets and linkage programs

We have used 22 chromosome 1 loci to construct a genetic linkage map of this autosome using the Venezuelan Reference Pedigree. These markers formed two linkage groups separated by an interval of more than 30 cM. Linkage maps were constructed separately using the computer programs LINKAGE and MAPMAKER to determine their relative speed, efficiency, and accuracy. We found that both programs generated maps with the same order and distances, although the LINKAGE program derived more information from the data, allowing placement of one additional marker. Many of the probes have previously been mapped using the CEPH pedigrees. However, the current map is generated from a different data set and so can be used to increase the certainty of locus order and map position. Ultimately, the generation and confirmation of a 1-cM map of this chromosome will require such multiple data sets.     

DNA array analysis in a Microsoft Windows environment.

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.     

KELVIN: a software package for rigorous measurement of statistical evidence in human genetics

This paper describes the software package KELVIN, which supports the PPL (posterior probability of linkage) framework for the measurement of statistical evidence in human (or more generally, diploid) genetic studies. In terms of scope, KELVIN supports two-point (trait-marker or marker-marker) and multipoint linkage analysis, based on either sex-averaged or sex-specific genetic maps, with an option to allow for imprinting; trait-marker linkage disequilibrium (LD), or association analysis, in case-control data, trio data, and/or multiplex family data, with options for joint linkage and trait-marker LD or conditional LD given linkage; dichotomous trait, quantitative trait and quantitative trait threshold models; and certain types of gene-gene interactions and covariate effects. Features and data (pedigree) structures can be freely mixed and matched within analyses. The statistical framework is specifically tailored to accumulate evidence in a mathematically rigorous way across multiple data sets or data subsets while allowing for multiple sources of heterogeneity, and KELVIN itself utilizes sophisticated software engineering to provide a powerful and robust platform for studying the genetics of complex disorders.     

非交叉配子形成体的连锁图谱构建方法

根据非交叉(achiasmatic)遗传模型,提出采用最大似然法计算遗传交换率的方法,同时开发了构建非交叉生物(F2群体)连锁图谱的计算机软件。通过卡方验检可测性连锁分子标记。对于无交叉生物现象,采用蒙特卡洛模拟技术,对交叉(chiasmatic)和非交叉两个遗传模型遗传交换率的估计值和作图效率进行了比较。模拟结果表明,非交叉模型能提供无偏的估计值,而交叉模型则只有实际值的一半。在所有同等的条件下,基于非交叉模型的作图效率均高于基于交叉模型(无校正)的作图效率。对于非交叉配子形成体,采用基于非交叉模型的交换率计算方法能获得理想的作图效率。     

构建分子标记连锁图谱的一种新方法：三点自交法

作者从数学上导出了基因作图的三点自交方法。这一方法同用三点测交法一样能提供各种作图信息,但不需要选育三隐性纯合基因亲本或品系,因而能大大提高作图功效。,从理论上证明,该方法也适合于小群体作图分子标记连锁图谱,同时用Ｆisher单一观察信息（即Ｆ信息）量证明,三点自交法是一种有效的作图方法,应用ＭＡＰＭＡＫＥＲ程序中所提供的才鼠Ｆ２群体中３３３个个体的１２个ＲＦＬＰ标记位点中前６个位点的数据对三点自交图图距计算具有与ＭＡＰＭＡＫＥＲ程序一样的功能,而且还提供了位点间的交叉干涉和位点的相引或相斥构型等信息以及紧密位点间发生负干涉作用的证据。     

PGAAS: a prokaryotic genome assembly assistant system

MOTIVATION: In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. RESULTS: We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. AVAILABILITY: We tested PGAAS on a Linux (Redhat 6.2) PC machine. It is developed with free software (MySQL, PHP and Apache). The whole package is distributed freely and can be downloaded as UNIX compress file: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.